New version: based on python 3

README.md

@@ -79,7 +79,8 @@ Asali has been tested on Ubuntu 16.04 LTS, Ubuntu 18.04 LTS, Windows 10, Windows
 ##### 2.1.1 Pre-requisites installation
 The Linux based external libraries can be installed by typing these commands:  
 `sudo apt-get update`  
-`sudo apt-get install git g++ gfortran python scons libboost-dev cython python-dev python-numpy python-numpy-dev python-setuptools cython python3 python3-dev python3-setuptools python3-numpy`  
+`sudo apt-get install scons git python3-ruamel.yaml python3-yaml g++ gfortran python libboost-dev cython python-dev python-numpy python-numpy-dev python-setuptools python3 python3-dev python3-setuptools python3-numpy cython3`  
+`sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 1`  
 
 ##### 2.1.2 How to install Gtkmm libraries
 [Gtkmm](https://www.gtkmm.org/en/) can be downloaded with the following command:  

Ubuntu/src/Asali.C

@@ -82,11 +82,11 @@ namespace ASALI
                     "<b>\nor select the default one (database/data.xml)</b>"
                     "\n\nLoading might take several minutes, depending"
                     "\non your system performances."),
-      bigLogo_("images/BigLogo.tiff"),
-      smallLogo1_("images/SmallLogo.tiff"),
-      smallLogo2_("images/SmallLogo.tiff"),
-      smallLogo3_("images/SmallLogo.tiff"),
-      smallLogo4_("images/SmallLogo.tiff")
+      bigLogo_("images/BigLogo.png"),
+      smallLogo1_("images/SmallLogo.png"),
+      smallLogo2_("images/SmallLogo.png"),
+      smallLogo3_("images/SmallLogo.png"),
+      smallLogo4_("images/SmallLogo.png")
     {
         #include "shared/Beer.H"
         #include "shared/BeerShort.H"
@@ -96,7 +96,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(grid_);

Ubuntu/src/asaliCatalystProperties.C

@@ -41,7 +41,7 @@
 namespace ASALI
 {
     asaliCatalystProperties::asaliCatalystProperties()
-    : het1dLogo_("images/Het1DLogo.tiff"),
+    : het1dLogo_("images/Het1DLogo.png"),
       mainBox_(Gtk::ORIENTATION_VERTICAL),
       rhoLabel_("Density"),
       condLabel_("Thermal conductivity"),
@@ -53,7 +53,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: catalyst input");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
 
         //Add background grid
         mainBox_.set_halign(Gtk::ALIGN_START);

Ubuntu/src/asaliKineticMaker.C

@@ -68,11 +68,11 @@ namespace ASALI
       typeLabel1_("Type"),  
       recapSpeciesLabel_("Species"),  
       recapReactionLabel_("Reactions"),  
-      logo1_("images/KineticSchemeLogo.tiff"),
-      logo2_("images/KineticSchemeLogo.tiff"),
-      logo3_("images/KineticSchemeLogo.tiff"),
-      logo4_("images/KineticSchemeLogo.tiff"),
-      logo5_("images/KineticSchemeLogo.tiff"),
+      logo1_("images/KineticSchemeLogo.png"),
+      logo2_("images/KineticSchemeLogo.png"),
+      logo3_("images/KineticSchemeLogo.png"),
+      logo4_("images/KineticSchemeLogo.png"),
+      logo5_("images/KineticSchemeLogo.png"),
       NR_(0),
       NC_(0),
       restart_(true)
@@ -96,7 +96,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Kinetic scheme");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(reactionNumberBox_);

Ubuntu/src/asaliPlot.C

@@ -54,7 +54,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: plotting");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
 
         //Add background grid
 

Ubuntu/src/asaliProperties.C

@@ -41,10 +41,10 @@
 namespace ASALI
 {
     asaliProperties::asaliProperties()
-    : batchLogo_("images/BatchLogo.tiff"),
-      ph1dLogo_("images/Ph1DLogo.tiff"),
-      het1dLogo_("images/Het1DLogo.tiff"),
-      pelletLogo_("images/PelletLogo.tiff"),
+    : batchLogo_("images/BatchLogo.png"),
+      ph1dLogo_("images/Ph1DLogo.png"),
+      het1dLogo_("images/Het1DLogo.png"),
+      pelletLogo_("images/PelletLogo.png"),
       mainBox_(Gtk::ORIENTATION_VERTICAL),
       nameLabel_("Name"),
       mwLabel_("Molecular weight"),
@@ -62,7 +62,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: properties input");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
 
         //Add background grid
         mainBox_.set_halign(Gtk::ALIGN_START);

Ubuntu/src/batchReactor.C

@@ -58,8 +58,8 @@ namespace ASALI
       timeLabel_("Integration time"),
       saveLabel_("Save solution every"),
       energyLabel_("Energy"),
-      logo1_("images/BatchLogo.tiff"),
-      logo2_("images/BatchLogo.tiff"),
+      logo1_("images/BatchLogo.png"),
+      logo2_("images/BatchLogo.png"),
       plotButtonBool_(false)
     {
 
@@ -70,7 +70,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Batch reactor");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(mainBox_);

Ubuntu/src/catalyticPellet.C

@@ -63,8 +63,8 @@ namespace ASALI
       pelletTypeLabel_("Pellet shape"),
       modelTypeLabel_("Diffusion model"),
       poreLabel_("Pore diameter"),
-      logo1_("images/PelletLogo.tiff"),
-      logo2_("images/PelletLogo.tiff"),
+      logo1_("images/PelletLogo.png"),
+      logo2_("images/PelletLogo.png"),
       pelletType_("none"),
       modelType_("none"),
       modelBool_(false),
@@ -79,7 +79,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Catalytic pellets");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(mainBox_);

Ubuntu/src/catalyticReactors.C

@@ -89,7 +89,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Catalytic reactors");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
         }
 
         //Species input menu

Ubuntu/src/chemkinConverter.C

@@ -45,7 +45,7 @@ namespace ASALI
       output_("Convert"),
       help_("Help"),
       exit_("Exit"),
-      logo_("images/SmallLogo.tiff")
+      logo_("images/SmallLogo.png")
     {
 
         #include "shared/Beer.H"
@@ -57,7 +57,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: CHEMKIN converter");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
 
 
         //Adding logo

Ubuntu/src/cstrReactor.C

@@ -59,8 +59,8 @@ namespace ASALI
       timeLabel_("Integration time"),
       saveLabel_("Save solution every"),
       energyLabel_("Energy"),
-      logo1_("images/CstrLogo.tiff"),
-      logo2_("images/CstrLogo.tiff"),
+      logo1_("images/CstrLogo.png"),
+      logo2_("images/CstrLogo.png"),
       plotButtonBool_(false)
     {
 
@@ -71,7 +71,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: CST reactor");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(mainBox_);

Ubuntu/src/equilibriumCalculator.C

@@ -60,7 +60,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Equilibrium calculator");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
             this->input();
         }
 

Ubuntu/src/het1dReactor.C

@@ -72,8 +72,8 @@ namespace ASALI
       honeyCombCPSILabel_("CPSI"),
       honeyCombWallThicknessLabel_("Wall thickness"),
       honeyCombDuctLabel_("Duct section"),
-      logo1_("images/Het1DLogo.tiff"),
-      logo2_("images/Het1DLogo.tiff"),
+      logo1_("images/Het1DLogo.png"),
+      logo2_("images/Het1DLogo.png"),
       reactorType_("none"),
       tubularBool_(false),
       honeyCombBool_(false),
@@ -88,7 +88,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: 1D HET reactor");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(mainBox_);

Ubuntu/src/ph1dReactor.C

@@ -62,8 +62,8 @@ namespace ASALI
       pointsLabel_("Number of points"),
       inertLabel_("Inert specie"),
       resolutionLabel_("Resolution type"),
-      logo1_("images/Ph1DLogo.png"),
-      logo2_("images/Ph1DLogo.png"),
+      logo1_("images/Ph1DLogo.tiff"),
+      logo2_("images/Ph1DLogo.tiff"),
       plotButtonBool_(false)
     {
 

Ubuntu/src/pressureDrops.C

@@ -61,8 +61,8 @@ namespace ASALI
       honeyCombWallThicknessLabel_("Wall thickness"),
       tubularDpLabel_("Bird R. B. et al. (1960)"),
       honeyCombDpLabel_("Bird R. B. et al. (1960)"),
-      logo1_("images/PressureLogo.tiff"),
-      logo2_("images/PressureLogo.tiff"),
+      logo1_("images/PressureLogo.png"),
+      logo2_("images/PressureLogo.png"),
       reactorType_("none"),
       tubularBool_(false),
       honeyCombBool_(false),
@@ -98,7 +98,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Pressure drops");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
             doneButton_.set_label("Next");
             this->input();
         }

Ubuntu/src/runBar.C

@@ -48,7 +48,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
         this->add(mainBox_);
         mainBox_.set_spacing(10);
         mainBox_.pack_start(solvingLabel_,Gtk::PACK_SHRINK);

Ubuntu/src/speciesPopup.C

@@ -49,7 +49,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: species names");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
         this->add(mainBox_);
         mainBox_.pack_start(scrolledWindow_);
         scrolledWindow_.add(speciesImage_);

Ubuntu/src/thermoTransportProperties.C

@@ -69,7 +69,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Thermodynamic and transport properties");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
             this->input();
         }
 

Ubuntu/src/transportProperties.C

@@ -71,7 +71,7 @@ namespace ASALI
             this->set_border_width(15);
             this->set_title("ASALI: Transport properties");
             this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-            this->set_icon_from_file("images/Icon.tiff");
+            this->set_icon_from_file("images/Icon.png");
 
             //Add background grid
             this->add(inputGrid_);

Ubuntu/src/vacuumProperties.C

@@ -74,7 +74,7 @@ namespace ASALI
         this->set_border_width(15);
         this->set_title("ASALI: Vacuum properties");
         this->set_position(Gtk::WIN_POS_CENTER_ALWAYS);
-        this->set_icon_from_file("images/Icon.tiff");
+        this->set_icon_from_file("images/Icon.png");
 
         this->add(grid_);