Some commenting added

include/EnergyLoss.h

@@ -46,6 +46,7 @@ class EnergyLoss {
 
     //constants for calculations
     static constexpr double MAX_FRACTIONAL_STEP = 0.001;
+    static constexpr double MAX_DEPTH = 50;
     static constexpr double MAX_H_E_PER_U = 100000.0;
     static constexpr double AVOGADRO = 0.60221367; //N_A times 10^(-24) for converting
     static constexpr double MEV2U = 1.0/931.4940954;

include/Nucleus.h

@@ -1,3 +1,11 @@
+/*
+	Nucleus.h
+	Nucleus is a derived class of Vec4. A nucleus is the kinematics is essentially a 4 vector with the
+	additional properties of the number of total nucleons (A), the number of protons (Z), a ground state mass,
+	an exctitation energy, and an isotopic symbol.
+
+	--GWM Jan 2021
+*/
 #ifndef NUCLEUS_H
 #define NUCLEUS_H
 
@@ -25,7 +33,8 @@ public:
 		return *this;
 	};
 
-	inline Nucleus operator+(const Nucleus& daughter) { 
+	//Conservation of nucleons and momentum
+	inline Nucleus operator+(const Nucleus& daughter) {
 		return Nucleus(GetZ()+daughter.GetZ(), GetA()+daughter.GetA(), GetPx()+daughter.GetPx(), GetPy()+daughter.GetPy(), GetPz()+daughter.GetPz(), GetE()+daughter.GetE()); 
 	};
 	inline Nucleus operator-(const Nucleus& daughter) {

include/Reaction.h

@@ -1,3 +1,11 @@
+/*
+	Reaction.h
+	Reaction is a class which implements either a decay or scattering reaction. As such it requires either
+	3 (decay) or 4 (scattering) nuclei to perform any calcualtions. I also links together the target, which provides
+	energy loss calculations, with the kinematics. Note that Reaction does not own the LayeredTarget.
+
+	--GWM Jan. 2021
+*/
 #ifndef REACTION_H
 #define REACTION_H
 
@@ -15,6 +23,8 @@ public:
 	void SetNuclei(int zt, int at, int zp, int ap, int ze, int ae);
 	void SetNuclei(const Nucleus* nucs);
 	void SetBeamKE(double bke);
+
+	/*Setters and getters*/
 	inline void SetLayeredTarget(LayeredTarget* targ) { target = targ; };
 	inline void SetPolarRxnAngle(double theta) { m_theta = theta; };
 	inline void SetAzimRxnAngle(double phi) { m_phi = phi; };

include/ReactionSystem.h

@@ -1,3 +1,11 @@
+/*
+	ReactionSystem.h
+	ReactionSystem is the base class from which all kinematics calculations should inherit. It contains all members and functions
+	to perform a single step reaction/decay, which is the basic building block of all subsequent types of reactions in MASK. More
+	complicated systems (see TwoStepSystem and ThreeStepSystem) add further data members and override the virtual functions.
+
+	--GWM Jan. 2021
+*/
 #ifndef REACTIONSYSTEM_H
 #define REACTIONSYSTEM_H
 
@@ -12,12 +20,16 @@ public:
 	ReactionSystem();
 	ReactionSystem(std::vector<int>& z, std::vector<int>& a);
 	virtual ~ReactionSystem();
+
 	virtual bool SetNuclei(std::vector<int>& z, std::vector<int>& a);
 	void AddTargetLayer(std::vector<int>& zt, std::vector<int>& at, std::vector<int>& stoich, double thickness);
+
+	/*Set sampling parameters*/
 	inline void SetRandomGenerator(TRandom3* gen) { generator = gen; gen_set_flag = true; };
 	inline void SetBeamDistro(double mean, double sigma) { m_beamDist = std::make_pair(mean, sigma); };
 	inline void SetTheta1Range(double min, double max) { m_theta1Range = std::make_pair(min*deg2rad, max*deg2rad); };
 	inline void SetExcitationDistro(double mean, double sigma) { m_exDist = std::make_pair(mean, sigma); };
+
 	virtual void RunSystem();
 
 	inline const Nucleus& GetTarget() const { return step1.GetTarget(); };
@@ -32,6 +44,8 @@ protected:
 	
 	Reaction step1;
 	LayeredTarget target;
+
+	//Sampling information
 	std::pair<double, double> m_beamDist, m_theta1Range, m_exDist;
 	TRandom3* generator; //not owned by ReactionSystem
 

input.txt

@@ -3,24 +3,25 @@ OutputFile: /media/gordon/b6414c35-ec1f-4fc1-83bc-a6b68ca4325a/gwm17/test_newkin
 SaveTree: yes
 SavePlots: yes
 ----------Reaction Information----------
-ReactionType: 0
+ReactionType: 2
 Z	A (order is target, projectile, ejectile, break1, break3)
-5	9
-0	0
-1	1
+5	10
+2	3
+2	4
+1	2
 ----------Target Information----------
 Name: test_targ
 Layers: 2
 ~Layer1
-Thickness(ug/cm^2): 0
+Thickness(ug/cm^2): 10
 Z	A	Stoich
 6	12	1
 0
 ~
 ~Layer2
-Thickness(ug/cm^2): 0
+Thickness(ug/cm^2): 80
 Z	A	Stoich
-5	9	1
+5	10	1
 0
 ~
 ----------Sampling Information----------

src/EnergyLoss.cpp

@@ -55,6 +55,8 @@ double EnergyLoss::GetEnergyLoss(int zp, int ap, double e_initial, double thickn
   double e_step = GetTotalStoppingPower(e_final)*x_step/1000.0; //initial step in e
   double e_threshold = 0.05*e_initial;
 
+  int depth=0;
+
   
   if(thickness == 0.0) return 0;
   else if(e_initial == 0.0) return 0;
@@ -62,16 +64,20 @@ double EnergyLoss::GetEnergyLoss(int zp, int ap, double e_initial, double thickn
   bool go = true;
   while(go) {
     //If intial guess of step size is too large, shrink until in range
-    if(e_step/e_final > MAX_FRACTIONAL_STEP /*&& e_step >= E_PRECISION_LIMIT*/) {
+    if(e_step/e_final > MAX_FRACTIONAL_STEP && depth < MAX_DEPTH) {
+      depth++;
       x_step *= 0.5;
       e_step = GetTotalStoppingPower(e_final)*x_step/1000.0;
     } else if((x_step + x_traversed) >= thickness) { //last chunk
       go = false;
       x_step = thickness - x_traversed; //get valid portion of last chunk
       e_final -= GetTotalStoppingPower(e_final)*x_step/1000.0;
+      if(depth > 20)std::cout<<"depth: "<<depth<<std::endl;
       if(e_final <= e_threshold) {
         return e_initial;
       }
+    } else if(depth == MAX_DEPTH) {
+      return e_initial;
     } else {
       x_traversed += x_step;
       e_step = GetTotalStoppingPower(e_final)*x_step/1000.0;

src/Nucleus.cpp

@@ -1,3 +1,11 @@
+/*
+	Nucleus.cpp
+	Nucleus is a derived class of Vec4. A nucleus is the kinematics is essentially a 4 vector with the
+	additional properties of the number of total nucleons (A), the number of protons (Z), a ground state mass,
+	an exctitation energy, and an isotopic symbol.
+
+	--GWM Jan 2021
+*/
 #include "Nucleus.h"
 #include "MassLookup.h"
 
@@ -13,7 +21,7 @@ Nucleus::Nucleus(int Z, int A) :
 {
 	m_gs_mass = MASS.FindMass(Z, A);
 	m_symbol = MASS.FindSymbol(Z, A);
-	SetVectorCartesian(0,0,0,m_gs_mass);
+	SetVectorCartesian(0,0,0,m_gs_mass); //by defualt a nucleus has mass given by the g.s.
 }
 
 Nucleus::Nucleus(int Z, int A, double px, double py, double pz, double E) :

src/Reaction.cpp

@@ -1,3 +1,11 @@
+/*
+	Reaction.cpp
+	Reaction is a class which implements either a decay or scattering reaction. As such it requires either
+	3 (decay) or 4 (scattering) nuclei to perform any calcualtions. I also links together the target, which provides
+	energy loss calculations, with the kinematics. Note that Reaction does not own the LayeredTarget.
+
+	--GWM Jan. 2021
+*/
 #include "Reaction.h"
 #include "KinematicsExceptions.h"
 
@@ -69,6 +77,7 @@ void Reaction::SetBeamKE(double bke) {
 	m_bke = bke - target->GetProjectileEnergyLoss(reactants[1].GetZ(), reactants[1].GetA(), bke, rxnLayer, 0);
 };
 
+//Methods given by Iliadis in Nuclear Physics of Stars, Appendix C
 void Reaction::CalculateReaction() {
 	//Target assumed at rest, with 0 excitation energy
 	reactants[0].SetVectorCartesian(0.,0.,0.,reactants[0].GetGroundStateMass());
@@ -112,6 +121,7 @@ void Reaction::CalculateReaction() {
 
 }
 
+//Calculate in CM, where decay is isotropic
 void Reaction::CalculateDecay() {
 
 	double Q = reactants[0].GetInvMass() - reactants[2].GetGroundStateMass() - reactants[3].GetGroundStateMass();