Merge pull request #91 from JETSCAPE/latessa/refactor-step

Refactoring Exec, Init, Clear, and Finish

.gitignore

@@ -9,6 +9,7 @@
 *.*~
 .DS_Store
 .vscode
+.bash_history
 html/*
 build*/*
 external_packages/LBT*

examples/unittests/LiquifierBase.cc

@@ -29,7 +29,7 @@ TEST(LiquefierBaseTest, TEST_add_a_droplet_and_Clear) {
     lqf.add_a_droplet(a_drop);
     EXPECT_EQ(1, lqf.get_dropletlist_size());
 
-    lqf.Clear();
+    lqf.ClearTask();
     EXPECT_EQ(0, lqf.get_dropletlist_size());
 }
 
@@ -134,7 +134,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_EQ(0, lqf.get_dropletlist_size());
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test when pOut == pIn (hard parton)
     pIn.push_back(test2);
@@ -145,7 +145,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_EQ(1, pOut.size());
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test when pOut == pIn (soft parton)
     pIn.push_back(test1);
@@ -159,7 +159,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_DOUBLE_EQ(x_test1.t(), (lqf.get_a_droplet(0).get_xmu())[0]);
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test a negative particle
     FourVector p_test3(3.0, 0.0, 0.0, 3.0);
@@ -176,7 +176,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_EQ(2, pOut.size());
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test a negative particle and a soft particle
     pIn.push_back(test2);
@@ -191,7 +191,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_EQ(3, pOut.size());
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test a negative particle and a hard particle
     pIn.push_back(test1);
@@ -209,7 +209,7 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     EXPECT_EQ(3, pOut.size());
     pIn.clear();
     pOut.clear();
-    lqf.Clear();
+    lqf.ClearTask();
 
     // test a soft particle in pIn only
     //pIn.push_back(test1);
@@ -222,5 +222,5 @@ TEST(LiquefierBaseTest, TEST_add_hydro_source) {
     //EXPECT_EQ(0, pOut.size());
     //pIn.clear();
     //pOut.clear();
-    //lqf.Clear();
+    //lqf.ClearTask();
 }

src/afterburner/SmashWrapper.cc

@@ -117,6 +117,7 @@ std::vector<std::vector<shared_ptr<Hadron>>> TestHadronList() {
 }
 
 void SmashWrapper::ExecuteTask() {
+  VERBOSE(2) << "SMASH afterburner running: " << GetId() << " ...";
   AfterburnerModus *modus = smash_experiment_->modus();
   // This is necessary to correctly handle indices of particle sets from hydro.
   // Every hydro event creates a new structure like jetscape_hadrons_

src/framework/Afterburner.cc

@@ -22,14 +22,14 @@ using namespace std;
 namespace Jetscape {
 void Afterburner::Init() {
   // Makes sure that XML file with options and parameters is loaded
-  JetScapeModuleBase::Init();
+  JetScapeModuleBase::InitTask();
   JSINFO << "Initializing Afterburner : " << GetId() << " ...";
   InitTask();
+  InitTasks();
 }
 
-void Afterburner::Exec() {
+void Afterburner::ExecuteTask() {
   VERBOSE(2) << "Afterburner running: " << GetId() << " ...";
-  ExecuteTask();
 }
 
 void Afterburner::CalculateTime() {

src/framework/Afterburner.h

@@ -38,9 +38,12 @@ class Afterburner : public JetScapeModuleBase {
     VERBOSE(8);
     disconnect_all();
   }
+  // Override Init here as function takes care of calling sub-tasks as well
+  virtual void Init() override;
+
+  // needs to be defined by afterburner modules
+  virtual void ExecuteTask();
 
-  virtual void Init();
-  virtual void Exec();
   virtual void CalculateTime();
 
   /// Fill in bulk media info for (t,x,y,z) from current hadron list (work in progress, see .cc file)

src/framework/BulkDynamicsManager.cc

@@ -35,56 +35,46 @@ BulkDynamicsManager::BulkDynamicsManager() : JetScapeModuleBase() {
 BulkDynamicsManager::~BulkDynamicsManager() {
   // Check if this is all really needed with shared_ptr ...
   JSDEBUG;
-  Clear();
+  ClearTask();
 
   if (GetNumberOfTasks() > 0)
     EraseTaskLast();
 }
 
-void BulkDynamicsManager::Clear() {
-  JSDEBUG << "BulkDynamicsManager clear() ...";
+void BulkDynamicsManager::ClearTask() {
+  JSDEBUG << "BulkDynamicsManager ClearTask() ...";
 
   int n = GetNumberOfTasks();
   for (int i = 1; i < n; i++)
     EraseTaskLast();
 
   // Clean Up not really working with iterators (see also above!!!) Some logic not clear for me.
   JetScapeSignalManager::Instance()->CleanUp();
-  JetScapeTask::ClearTasks();
-
 }
 
-void BulkDynamicsManager::Init() {
+void BulkDynamicsManager::InitTask() {
   JSINFO << "Intialize BulkDynamicsManager ...";
 
+  //Critical temperature to switch from hydro to something else
+  Tc = GetXMLElementDouble({"BDM", "Tc"});
+
   if (GetNumberOfTasks() < 1) {
     JSWARN << " : No valid bulk dynamics Manager modules found ...";
     exit(-1);
   }
 
   JSINFO << "Found " << GetNumberOfTasks()
          << " Bulk Dynamics Manager Tasks/Modules Initialize them ... ";
-
-  //Critical temperature to switch from hydro to something else
-  Tc = GetXMLElementDouble({"BDM", "Tc"});
-
-  BulkDynamicsManager::InitTasks();
-
 }
-void BulkDynamicsManager::Exec() {
+
+void BulkDynamicsManager::ExecuteTask() {
   VERBOSE(1) << "Run BulkDynamicsManager Manager ...";
   JSDEBUG << "Task Id = " << this_thread::get_id();
 
   if (GetNumberOfTasks() < 1) {
     JSWARN << " : No valid Bulk Dynamics Manager modules found ...";
     exit(-1);
   }
-
-  JetScapeTask::ExecuteTasks();
-
-  //
-  VERBOSE(3) << " " << GetNumberOfTasks()
-             << " Bulk Dynamics Manager Tasks/Modules finished.";
 }
 
 void BulkDynamicsManager::CalculateTime()
@@ -154,7 +144,7 @@ void BulkDynamicsManager::FinishPerEvent()
   JetScapeModuleBase::FinishPerEventTasks();
 
   //JP: Quick fix, to be discussed, similar to writer, clear is only called for active tasks, so call here directly ...
-  Clear();
+  ClearTask();
 }
 
 void BulkDynamicsManager::UpdateEnergyDepositFromModules(int t, double edop){

src/framework/BulkDynamicsManager.h

@@ -44,15 +44,15 @@ class BulkDynamicsManager
 
   /** It initializes the tasks attached to the bulk dynamics manager.
    */
-  virtual void Init();
+  virtual void InitTask();
 
   /**
   */
-  virtual void Exec();
+  virtual void ExecuteTask();
 
   /** It erases the tasks attached with the bulk dynamics manager. It can be overridden by other tasks.
    */
-  virtual void Clear();
+  virtual void ClearTask();
 
   virtual void CalculateTime();
 

src/framework/BulkMediaBase.cc

@@ -19,18 +19,18 @@
 
 using namespace std;
 
-namespace Jetscape {  
+namespace Jetscape {
 void BulkMediaBase::Init() {
   // Makes sure that XML file with options and parameters is loaded
-  JetScapeModuleBase::Init();
+  JetScapeModuleBase::InitTask();
   JSINFO << "Initializing BulkMediaBase : " << GetId() << " ...";
 
   InitTask();
+  InitTasks();
 }
 
-void BulkMediaBase::Exec() {
+void BulkMediaBase::ExecuteTask() {
   VERBOSE(2) << "BulkMediaBase running: " << GetId() << " ...";
-  ExecuteTask();
 }
 
 void BulkMediaBase::CalculateTime() {

src/framework/BulkMediaBase.h

@@ -38,8 +38,10 @@ class BulkMediaBase : public JetScapeModuleBase {
     disconnect_all();
   }
 
-  virtual void Init();
-  virtual void Exec();
+  // Override Init here as function takes care of calling sub-tasks as well
+  void Init() override;
+
+  virtual void ExecuteTask();
   virtual void CalculateTime();
   virtual void GetBulkInfo(Jetscape::real t, Jetscape::real x, Jetscape::real y,Jetscape::real z,
 			   std::unique_ptr<BulkMediaInfo> &bulk_info_ptr){}

src/framework/FluidDynamics.cc

@@ -2,7 +2,7 @@
  * Copyright (c) The JETSCAPE Collaboration, 2018
  *
  * Modular, task-based framework for simulating all aspects of heavy-ion collisions
- * 
+ *
  * For the list of contributors see AUTHORS.
  *
  * Report issues at https://github.com/JETSCAPE/JETSCAPE/issues
@@ -41,7 +41,7 @@ FluidDynamics::~FluidDynamics() {
 }
 
 void FluidDynamics::Init() {
-  JetScapeModuleBase::Init();
+  JetScapeModuleBase::InitTask();
 
   JSINFO << "Initialize FluidDynamics : " << GetId() << " ...";
 
@@ -60,12 +60,12 @@ void FluidDynamics::Init() {
   }
 
   InitializeHydro(parameter_list);
-  InitTask();
 
-  JetScapeTask::InitTasks();
+  InitTask();
+  InitTasks();
 }
 
-void FluidDynamics::Exec() {
+void FluidDynamics::ExecuteTask() {
   VERBOSE(2) << "Run Hydro : " << GetId() << " ...";
   VERBOSE(8) << "Current Event #" << GetCurrentEvent();
 
@@ -75,13 +75,12 @@ void FluidDynamics::Exec() {
   }
 
   EvolveHydro();
-  JetScapeTask::ExecuteTasks();
 }
 
-void FluidDynamics::Clear() {
+void FluidDynamics::ClearTask() {
   clear_up_evolution_data();
   if (!weak_ptr_is_uninitialized(liquefier_ptr)) {
-    liquefier_ptr.lock()->Clear();
+    liquefier_ptr.lock()->ClearTask();
   }
 }
 

src/framework/FluidDynamics.h

@@ -83,17 +83,17 @@ class FluidDynamics : public JetScapeModuleBase {
   /** Default destructor. */
   virtual ~FluidDynamics();
 
-  /** Reads the input parameters from the XML file under the tag <Hydro>. Uses JetScapeSingnalManager Instance to retrive the Initial State Physics information. Calls InitializeHydro(parameter_list) and InitTask(); This explicit call can be used for actual initialization of modules such as @a Brick, @a MpiMusic, or @a OSU-HYDRO if attached as a @a polymorphic class. It also initializes the tasks within the current module.   
-	@sa Read about @a polymorphism in C++.
+  /** Reads the input parameters from the XML file under the tag <Hydro>. Uses JetScapeSingnalManager Instance to retrive the Initial State Physics information. Calls InitializeHydro(parameter_list) and InitTask(); This explicit call can be used for actual initialization of modules such as @a Brick, @a MpiMusic, or @a OSU-HYDRO if attached as a @a polymorphic class. It also initializes the tasks within the current module.
+	@sa Read about @a polymorphism in C++. Override Init (not InitTask) here as sub-tasks are called as well.
     */
-  virtual void Init();
+  void Init() override;
 
   /** Calls EvolveHydro(); This explicit call can be used for actual execution of hydrodynamic evolution defined in the modules such as @a Brick, @a MpiMusic, or @a OSU-HYDRO if attached as a @a polymorphic class. It also execute the tasks within the current module.
 	@sa Read about @a polymorphism in C++.
     */
-  virtual void Exec();
+  virtual void ExecuteTask();
 
-  virtual void Clear();
+  virtual void ClearTask();
 
   /** @return parameter_list A pointer to the class Parameter which contains a file name for the fluid dynamics task.
 	@sa Implementation of the class Parameter.

src/framework/Hadronization.cc

@@ -34,13 +34,13 @@ Hadronization::Hadronization() {
 
 Hadronization::~Hadronization() {}
 
-void Hadronization::Clear() {
+void Hadronization::ClearTask() {
   VERBOSESHOWER(8);
   outHadrons.clear();
 }
 
-void Hadronization::Init() {
-  JetScapeModuleBase::Init();
+void Hadronization::InitTask() {
+  JetScapeModuleBase::InitTask();
 
   // May need to read some configuration info from XML file here
 
@@ -52,7 +52,6 @@ void Hadronization::Init() {
   JSINFO << "Found " << GetNumberOfTasks()
          << " Hadronization Tasks/Modules Initialize them ... ";
   VERBOSE(2) << " Module Found is " << GetTaskList()[0]->GetId();
-  JetScapeTask::InitTasks();
 }
 
 void Hadronization::DoHadronize() {
@@ -66,7 +65,7 @@ void Hadronization::DoHadronize() {
   }
 }
 
-void Hadronization::Exec() {
+void Hadronization::ExecuteTask() {
   VERBOSE(2) << "Run Hadronization Exec...";
   VERBOSE(2) << "Found " << GetNumberOfTasks()
              << " Hadronization Tasks/Modules Execute them ... ";

src/framework/Hadronization.h

@@ -2,7 +2,7 @@
  * Copyright (c) The JETSCAPE Collaboration, 2018
  *
  * Modular, task-based framework for simulating all aspects of heavy-ion collisions
- * 
+ *
  * For the list of contributors see AUTHORS.
  *
  * Report issues at https://github.com/JETSCAPE/JETSCAPE/issues
@@ -33,13 +33,13 @@ class Hadronization : public JetScapeModuleBase,
   Hadronization();
   virtual ~Hadronization();
   virtual shared_ptr<Hadronization> Clone() const { return nullptr; }
-  virtual void Init();
-  virtual void Exec();
+  virtual void InitTask();
+  virtual void ExecuteTask();
   virtual void DoHadronization(vector<vector<shared_ptr<Parton>>> &pIn,
                                vector<shared_ptr<Hadron>> &hOut,
                                vector<shared_ptr<Parton>> &pOut){};
   virtual void WriteTask(weak_ptr<JetScapeWriter> w);
-  virtual void Clear();
+  virtual void ClearTask();
 
   void GetHadrons(vector<shared_ptr<Hadron>>& signal){signal = outHadrons;}
   sigslot::signal3<vector<vector<shared_ptr<Parton>>> &,