CLI::Timer renamed to remove compiler errors

doc/Doxyfile

@@ -822,7 +822,8 @@ WARN_LOGFILE           =
 INPUT                  = $(pFlow_PROJECT_DIR)/src \
                          $(pFlow_PROJECT_DIR)/utilities \
                          $(pFlow_PROJECT_DIR)/solvers \
-                         mdDocs
+                         mdDocs \
+                         $(pFlow_PROJECT_DIR)/tutorials
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -866,7 +867,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = $(pFlow_PROJECT_DIR)/src/phasicFlow/commandLine
+EXCLUDE                = $(pFlow_PROJECT_DIR)/src/phasicFlow/commandLine/CLI
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

doc/mdDocs/howToBuild.md

@@ -123,17 +123,19 @@ After building, `bin`, `include`, and `lib` folders will be created in `~/Phasic
 
 **note 1**: When compiling the code in parallel, you need to have enough RAM on your computer. As a rule, you need 1 GB free RAM per each processor in your computer for compiling in parallel.
 You may want to use fewer number of cores on your computer by using the following command:
+
 `$ make install -j 3`
-the above command uses only 3 cores for compiling. 
+
+the above command only uses 3 cores for compiling. 
 
 **note 2**: By default PhasicFlow is compiled with **double** as floating point variable. You can compile it with **float**. Just in the command line of camke added `-DpFlow_Build_Double=Off` flag to compile it with float. For example if you are building for cuda, you can enter the following command:
 
-`$ cmake ../ -DpFlow_Build_Cuda=On --DpFlow_Build_Double=Off`
+`$ cmake ../ -DpFlow_Build_Cuda=On -DpFlow_Build_Double=Off`
 
 ### Step 6: Testing
 In the current terminal or a new terminal enter the following command:
 
-`$ ~checkPhasicFlow`
+`$ checkPhasicFlow`
 
 This command shows the host and device environments and software version. If PhasicFlow was build correctly, you would get the following output:
 ```

doc/mdDocs/howToUsePhasicFlow.md

@@ -0,0 +1,5 @@
+# How to use PhasicFlow {#howToUsePhasicFlow}
+Here you will learn how to use PhasicFlow to setup a granular flow simulation. The inputs for simulation are supplied through some text-based files, called file dictionary, located in two folders: `settings` and `caseSetup`. These folders are located under the root case directory. 
+All the commands are performed through terminal in which the current working directory is root case directory (you see `settings` and `caseSetup` folders when `ls` command is entered). The states of geometry and particles are stored in time folders with names that represent the time. When simulation is finished, one case use post-processing tool pFlowToVTK to convert the stored results in the time folder into VTK file format. The VTK file format can be read by Paraview. 
+A set of tutorials with detailed descriptions are provided to show you how to use PhasicFlow for various granular flow problems. Here is a list of them.
+* [Small rotating drum] (@ref rotatingDrumSmall)

src/phasicFlow/commandLine/CLI/cliTimer.hpp

@@ -22,7 +22,7 @@
 namespace CLI {
 
 /// This is a simple timer with pretty printing. Creating the timer starts counting.
-class Timer {
+class cliTimer {
   protected:
     /// This is a typedef to make clocks easier to use
     using clock = std::chrono::steady_clock;
@@ -57,7 +57,7 @@ class Timer {
 
   public:
     /// Standard constructor, can set title and print function
-    explicit Timer(std::string title = "Timer", time_print_t time_print = Simple)
+    explicit cliTimer(std::string title = "cliTimer", time_print_t time_print = Simple)
         : title_(std::move(title)), time_print_(std::move(time_print)), start_(clock::now()) {}
 
     /// Time a function by running it multiple times. Target time is the len to target.
@@ -111,17 +111,17 @@ class Timer {
     std::string to_string() const { return time_print_(title_, make_time_str()); }
 
     /// Division sets the number of cycles to divide by (no graphical change)
-    Timer &operator/(std::size_t val) {
+    cliTimer &operator/(std::size_t val) {
         cycles = val;
         return *this;
     }
 };
 
 /// This class prints out the time upon destruction
-class AutoTimer : public Timer {
+class AutoTimer : public cliTimer {
   public:
     /// Reimplementing the constructor is required in GCC 4.7
-    explicit AutoTimer(std::string title = "Timer", time_print_t time_print = Simple) : Timer(title, time_print) {}
+    explicit AutoTimer(std::string title = "cliTimer", time_print_t time_print = Simple) : cliTimer(title, time_print) {}
     // GCC 4.7 does not support using inheriting constructors.
 
     /// This destructor prints the string
@@ -131,4 +131,4 @@ class AutoTimer : public Timer {
 }  // namespace CLI
 
 /// This prints out the time if shifted into a std::cout like stream.
-inline std::ostream &operator<<(std::ostream &in, const CLI::Timer &timer) { return in << timer.to_string(); }
+inline std::ostream &operator<<(std::ostream &in, const CLI::cliTimer &timer) { return in << timer.to_string(); }

tutorials/sphereGranFlow/rotatingDrumSmall/README.md

@@ -1,3 +1,4 @@
+# Simulating a small rotating drum {#rotatingDrumSmall}
 ## Problem definition
 The problem is to simulate a rotating drum with the diameter 0.24 m and the length 0.1 m rotating at 11.6 rpm. It is filled with 30,000 4-mm spherical particles. The timestep for integration is 0.00001 s.
 <div align="center"><b>