Re-organize the files, implement the CoolProp and revise the liquid/gas interface temperature BC

CMakeLists.txt

@@ -0,0 +1,38 @@
+cmake_minimum_required(VERSION 3.0.0)
+project(demo)
+
+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(CANTERA_INCLUDES ${CANTERA_DIR}/include)
+set(IDA_INCLUDES ${IDA_DIR}/include)
+set(GSL_INCLUDES /usr/include/gsl)
+set(COOLPROP_INCLUDES ${COOLPROP_DIR}/include)
+set(FMT_INCLUDES ${FMT_DIR}/include)
+
+# Search for source files
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+add_executable(DropletCombustion ${SRC_LIST})
+
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+set(CMAKE_INSTALL_RPATH "${IDA_DIR}/lib;${CANTERA_DIR}/lib;${COOLPROP_DIR}/lib;${FMT_DIR}/lib")
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+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})
+
+# Set the output path
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/bin)

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+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#elif defined(__WATCOMC__)
+# if defined(__LINUX__)
+#  define PLATFORM_ID "Linux"
+
+# elif defined(__DOS__)
+#  define PLATFORM_ID "DOS"
+
+# elif defined(__OS2__)
+#  define PLATFORM_ID "OS2"
+
+# elif defined(__WINDOWS__)
+#  define PLATFORM_ID "Windows3x"
+
+# else /* unknown platform */
+#  define PLATFORM_ID
+# endif
+
+#elif defined(__INTEGRITY)
+# if defined(INT_178B)
+#  define PLATFORM_ID "Integrity178"
+
+# else /* regular Integrity */
+#  define PLATFORM_ID "Integrity"
+# endif
+
+#else /* unknown platform */
+# define PLATFORM_ID
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM64)
+#  define ARCHITECTURE_ID "ARM64"
+
+# elif defined(_M_ARM)
+#  if _M_ARM == 4
+#   define ARCHITECTURE_ID "ARMV4I"
+#  elif _M_ARM == 5
+#   define ARCHITECTURE_ID "ARMV5I"
+#  else
+#   define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM)
+#  endif
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__WATCOMC__)
+# if defined(_M_I86)
+#  define ARCHITECTURE_ID "I86"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC)
+# if defined(__ICCARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__ICCRX__)
+#  define ARCHITECTURE_ID "RX"
+
+# elif defined(__ICCRH850__)
+#  define ARCHITECTURE_ID "RH850"
+
+# elif defined(__ICCRL78__)
+#  define ARCHITECTURE_ID "RL78"
+
+# elif defined(__ICCRISCV__)
+#  define ARCHITECTURE_ID "RISCV"
+
+# elif defined(__ICCAVR__)
+#  define ARCHITECTURE_ID "AVR"
+
+# elif defined(__ICC430__)
+#  define ARCHITECTURE_ID "MSP430"
+
+# elif defined(__ICCV850__)
+#  define ARCHITECTURE_ID "V850"
+
+# elif defined(__ICC8051__)
+#  define ARCHITECTURE_ID "8051"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__ghs__)
+# if defined(__PPC64__)
+#  define ARCHITECTURE_ID "PPC64"
+
+# elif defined(__ppc__)
+#  define ARCHITECTURE_ID "PPC"
+
+# elif defined(__ARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__x86_64__)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(__i386__)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+#else
+#  define ARCHITECTURE_ID
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number components. */
+#ifdef COMPILER_VERSION_MAJOR
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct a string literal encoding the internal version number. */
+#ifdef COMPILER_VERSION_INTERNAL
+char const info_version_internal[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_',
+  'i','n','t','e','r','n','a','l','[',
+  COMPILER_VERSION_INTERNAL,']','\0'};
+#endif
+
+/* Construct a string literal encoding the version number components. */
+#ifdef SIMULATE_VERSION_MAJOR
+char const info_simulate_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[',
+  SIMULATE_VERSION_MAJOR,
+# ifdef SIMULATE_VERSION_MINOR
+  '.', SIMULATE_VERSION_MINOR,
+#  ifdef SIMULATE_VERSION_PATCH
+   '.', SIMULATE_VERSION_PATCH,
+#   ifdef SIMULATE_VERSION_TWEAK
+    '.', SIMULATE_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+
+#if !defined(__STDC__)
+# if (defined(_MSC_VER) && !defined(__clang__)) \
+  || (defined(__ibmxl__) || defined(__IBMC__))
+#  define C_DIALECT "90"
+# else
+#  define C_DIALECT
+# endif
+#elif __STDC_VERSION__ >= 201000L
+# define C_DIALECT "11"
+#elif __STDC_VERSION__ >= 199901L
+# define C_DIALECT "99"
+#else
+# define C_DIALECT "90"
+#endif
+const char* info_language_dialect_default =
+  "INFO" ":" "dialect_default[" C_DIALECT "]";
+
+/*--------------------------------------------------------------------------*/
+
+#ifdef ID_VOID_MAIN
+void main() {}
+#else
+# if defined(__CLASSIC_C__)
+int main(argc, argv) int argc; char *argv[];
+# else
+int main(int argc, char* argv[])
+# endif
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+  require += info_arch[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
+#ifdef COMPILER_VERSION_INTERNAL
+  require += info_version_internal[argc];
+#endif
+#ifdef SIMULATE_ID
+  require += info_simulate[argc];
+#endif
+#ifdef SIMULATE_VERSION_MAJOR
+  require += info_simulate_version[argc];
+#endif
+#if defined(__CRAYXE) || defined(__CRAYXC)
+  require += info_cray[argc];
+#endif
+  require += info_language_dialect_default[argc];
+  (void)argv;
+  return require;
+}
+#endif

build/CMakeFiles/3.16.4/CompilerIdCXX/CMakeCXXCompilerId.cpp

@@ -0,0 +1,660 @@
+/* This source file must have a .cpp extension so that all C++ compilers
+   recognize the extension without flags.  Borland does not know .cxx for
+   example.  */
+#ifndef __cplusplus
+# error "A C compiler has been selected for C++."
+#endif
+
+
+/* Version number components: V=Version, R=Revision, P=Patch
+   Version date components:   YYYY=Year, MM=Month,   DD=Day  */
+
+#if defined(__COMO__)
+# define COMPILER_ID "Comeau"
+  /* __COMO_VERSION__ = VRR */
+# define COMPILER_VERSION_MAJOR DEC(__COMO_VERSION__ / 100)
+# define COMPILER_VERSION_MINOR DEC(__COMO_VERSION__ % 100)
+
+#elif defined(__INTEL_COMPILER) || defined(__ICC)
+# define COMPILER_ID "Intel"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# if defined(__GNUC__)
+#  define SIMULATE_ID "GNU"
+# endif
+  /* __INTEL_COMPILER = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100)
+# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10)
+# if defined(__INTEL_COMPILER_UPDATE)
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER_UPDATE)
+# else
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER   % 10)
+# endif
+# if defined(__INTEL_COMPILER_BUILD_DATE)
+  /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */
+#  define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE)
+# endif
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+# if defined(__GNUC__)
+#  define SIMULATE_VERSION_MAJOR DEC(__GNUC__)
+# elif defined(__GNUG__)
+#  define SIMULATE_VERSION_MAJOR DEC(__GNUG__)
+# endif
+# if defined(__GNUC_MINOR__)
+#  define SIMULATE_VERSION_MINOR DEC(__GNUC_MINOR__)
+# endif
+# if defined(__GNUC_PATCHLEVEL__)
+#  define SIMULATE_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(__PATHCC__)
+# define COMPILER_ID "PathScale"
+# define COMPILER_VERSION_MAJOR DEC(__PATHCC__)
+# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__)
+# if defined(__PATHCC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__)
+# endif
+
+#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__)
+# define COMPILER_ID "Embarcadero"
+# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF)
+# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF)
+# define COMPILER_VERSION_PATCH DEC(__CODEGEARC_VERSION__     & 0xFFFF)
+
+#elif defined(__BORLANDC__)
+# define COMPILER_ID "Borland"
+  /* __BORLANDC__ = 0xVRR */
+# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8)
+# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF)
+
+#elif defined(__WATCOMC__) && __WATCOMC__ < 1200
+# define COMPILER_ID "Watcom"
+   /* __WATCOMC__ = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__WATCOMC__)
+# define COMPILER_ID "OpenWatcom"
+   /* __WATCOMC__ = VVRP + 1100 */
+# define COMPILER_VERSION_MAJOR DEC((__WATCOMC__ - 1100) / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__SUNPRO_CC)
+# define COMPILER_ID "SunPro"
+# if __SUNPRO_CC >= 0x5100
+   /* __SUNPRO_CC = 0xVRRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>12)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xFF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# else
+   /* __SUNPRO_CC = 0xVRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>8)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# endif
+
+#elif defined(__HP_aCC)
+# define COMPILER_ID "HP"
+  /* __HP_aCC = VVRRPP */
+# define COMPILER_VERSION_MAJOR DEC(__HP_aCC/10000)
+# define COMPILER_VERSION_MINOR DEC(__HP_aCC/100 % 100)
+# define COMPILER_VERSION_PATCH DEC(__HP_aCC     % 100)
+
+#elif defined(__DECCXX)
+# define COMPILER_ID "Compaq"
+  /* __DECCXX_VER = VVRRTPPPP */
+# define COMPILER_VERSION_MAJOR DEC(__DECCXX_VER/10000000)
+# define COMPILER_VERSION_MINOR DEC(__DECCXX_VER/100000  % 100)
+# define COMPILER_VERSION_PATCH DEC(__DECCXX_VER         % 10000)
+
+#elif defined(__IBMCPP__) && defined(__COMPILER_VER__)
+# define COMPILER_ID "zOS"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__ibmxl__) && defined(__clang__)
+# define COMPILER_ID "XLClang"
+# define COMPILER_VERSION_MAJOR DEC(__ibmxl_version__)
+# define COMPILER_VERSION_MINOR DEC(__ibmxl_release__)
+# define COMPILER_VERSION_PATCH DEC(__ibmxl_modification__)
+# define COMPILER_VERSION_TWEAK DEC(__ibmxl_ptf_fix_level__)
+
+
+#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ >= 800
+# define COMPILER_ID "XL"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ < 800
+# define COMPILER_ID "VisualAge"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE_MAJOR)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__FUJITSU) || defined(__FCC_VERSION) || defined(__fcc_version)
+# define COMPILER_ID "Fujitsu"
+
+#elif defined(__ghs__)
+# define COMPILER_ID "GHS"
+/* __GHS_VERSION_NUMBER = VVVVRP */
+# ifdef __GHS_VERSION_NUMBER
+# define COMPILER_VERSION_MAJOR DEC(__GHS_VERSION_NUMBER / 100)
+# define COMPILER_VERSION_MINOR DEC(__GHS_VERSION_NUMBER / 10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__GHS_VERSION_NUMBER      % 10)
+# endif
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__ARMCC_VERSION) && !defined(__clang__)
+# define COMPILER_ID "ARMCC"
+#if __ARMCC_VERSION >= 1000000
+  /* __ARMCC_VERSION = VRRPPPP */
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/1000000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 100)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION     % 10000)
+#else
+  /* __ARMCC_VERSION = VRPPPP */
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/100000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 10)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION    % 10000)
+#endif
+
+
+#elif defined(__clang__) && defined(__apple_build_version__)
+# define COMPILER_ID "AppleClang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__)
+
+#elif defined(__clang__) && defined(__ARMCOMPILER_VERSION)
+# define COMPILER_ID "ARMClang"
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCOMPILER_VERSION/1000000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCOMPILER_VERSION/10000 % 100)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCOMPILER_VERSION     % 10000)
+# define COMPILER_VERSION_INTERNAL DEC(__ARMCOMPILER_VERSION)
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__GNUC__) || defined(__GNUG__)
+# define COMPILER_ID "GNU"
+# if defined(__GNUC__)
+#  define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# else
+#  define COMPILER_VERSION_MAJOR DEC(__GNUG__)
+# endif
+# if defined(__GNUC_MINOR__)
+#  define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# endif
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+#elif defined(__VISUALDSPVERSION__) || defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__)
+# define COMPILER_ID "ADSP"
+#if defined(__VISUALDSPVERSION__)
+  /* __VISUALDSPVERSION__ = 0xVVRRPP00 */
+# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24)
+# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF)
+# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8  & 0xFF)
+#endif
+
+#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+# if defined(__VER__) && defined(__ICCARM__)
+#  define COMPILER_VERSION_MAJOR DEC((__VER__) / 1000000)
+#  define COMPILER_VERSION_MINOR DEC(((__VER__) / 1000) % 1000)
+#  define COMPILER_VERSION_PATCH DEC((__VER__) % 1000)
+#  define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__)
+# elif defined(__VER__) && (defined(__ICCAVR__) || defined(__ICCRX__) || defined(__ICCRH850__) || defined(__ICCRL78__) || defined(__ICC430__) || defined(__ICCRISCV__) || defined(__ICCV850__) || defined(__ICC8051__))
+#  define COMPILER_VERSION_MAJOR DEC((__VER__) / 100)
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+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... rebuild_cache"
+	@echo "... DropletCombustion"
+	@echo "... edit_cache"
+	@echo "... src/UserData.o"
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+	@echo "... src/UserData.s"
+	@echo "... src/gridRoutines.o"
+	@echo "... src/gridRoutines.i"
+	@echo "... src/gridRoutines.s"
+	@echo "... src/main.o"
+	@echo "... src/main.i"
+	@echo "... src/main.s"
+	@echo "... src/parse.o"
+	@echo "... src/parse.i"
+	@echo "... src/parse.s"
+	@echo "... src/residue.o"
+	@echo "... src/residue.i"
+	@echo "... src/residue.s"
+	@echo "... src/solution.o"
+	@echo "... src/solution.i"
+	@echo "... src/solution.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
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+	$(CMAKE_COMMAND) -S$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+

build/cmake_install.cmake

@@ -0,0 +1,49 @@
+# Install script for directory: /backup/weiye/src_binary_droplet
+
+# Set the install prefix
+if(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  set(CMAKE_INSTALL_PREFIX "/usr/local")
+endif()
+string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  if(BUILD_TYPE)
+    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  else()
+    set(CMAKE_INSTALL_CONFIG_NAME "")
+  endif()
+  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+endif()
+
+# Set the component getting installed.
+if(NOT CMAKE_INSTALL_COMPONENT)
+  if(COMPONENT)
+    message(STATUS "Install component: \"${COMPONENT}\"")
+    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  else()
+    set(CMAKE_INSTALL_COMPONENT)
+  endif()
+endif()
+
+# Install shared libraries without execute permission?
+if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+  set(CMAKE_INSTALL_SO_NO_EXE "0")
+endif()
+
+# Is this installation the result of a crosscompile?
+if(NOT DEFINED CMAKE_CROSSCOMPILING)
+  set(CMAKE_CROSSCOMPILING "FALSE")
+endif()
+
+if(CMAKE_INSTALL_COMPONENT)
+  set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
+else()
+  set(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
+endif()
+
+string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
+       "${CMAKE_INSTALL_MANIFEST_FILES}")
+file(WRITE "/backup/weiye/src_binary_droplet/build/${CMAKE_INSTALL_MANIFEST}"
+     "${CMAKE_INSTALL_MANIFEST_CONTENT}")

include/UserData.h

@@ -0,0 +1,221 @@
+#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
+

include/gridRoutines.h

@@ -0,0 +1,89 @@
+#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

include/macros.h

@@ -0,0 +1,82 @@
+#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)
+
+#define ONE_ATM RCONST(101325.0)
+
+/* 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

include/parse.h

@@ -0,0 +1,36 @@
+#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
+
+

include/parse.hpp

@@ -0,0 +1,75 @@
+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);
+}

include/residue.h

@@ -0,0 +1,129 @@
+#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
+
+#ifndef COOLPROP_DEF
+#define COOLPROP_DEF
+#include <CoolProp.h>   //for gas-phase thermodynamic properties
+//#include <HumidAirProp.h>
+//#include <CPState.h>
+#endif
+
+#include "UserData.h"
+#include <vector> //add the vector module
+
+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,const double* ydata);
+
+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);
+
+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);

include/solution.h

@@ -0,0 +1,15 @@
+#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);

include/timing.h

@@ -0,0 +1,2 @@
+double get_wall_time();
+double get_cpu_time();

include/timing.hpp

@@ -0,0 +1,45 @@
+//  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

src/UserData.cpp

@@ -0,0 +1,499 @@
+#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;
+}
+

src/gridRoutines.cpp

@@ -0,0 +1,293 @@
+#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);
+}
+

src/main.cpp

@@ -0,0 +1,503 @@
+/*
+ _____ ___  ____   ____ 
+|_   _/ _ \|  _ \ / ___|
+  | || | | | |_) | |    
+  | || |_| |  _ <| |___ 
+  |_| \___/|_| \_\\____|
+                        
+*/
+
+#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);
+
+//     /**************** 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);
+
+	ier=setAlgebraicVariables(&id,data,ydata);
+
+	////////// 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;
+        int 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);
+					}
+
+				}
+			}
+            
+			/*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));
+
+            /*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);
+}

src/parse.cpp

@@ -0,0 +1,79 @@
+#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);
+}

src/solution.cpp

@@ -0,0 +1,90 @@
+#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");
+}