From 1a100005560100df8609350f3bb6c479d8759358 Mon Sep 17 00:00:00 2001
From: Gordon McCann <gmccann@fsu.edu>
Date: Fri, 8 Oct 2021 15:41:23 -0400
Subject: [PATCH] Modified reading in of layered target data to be more
 intuitive, which lead to finding and fixing a bug in the logic for handling
 zero thickness or zero energy EnergyLoss::GetEnergyLoss calls

---
 include/KinematicsExceptions.h |  6 ++----
 input.txt                      | 17 ++++++++---------
 src/EnergyLoss.cpp             |  9 ++++-----
 src/MaskApp.cpp                | 16 ++++++++++------
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/include/KinematicsExceptions.h b/include/KinematicsExceptions.h
index 76ed6f1..3153a18 100644
--- a/include/KinematicsExceptions.h
+++ b/include/KinematicsExceptions.h
@@ -14,15 +14,13 @@
 */
 struct ELossException : public std::exception {
 	ELossException(const std::string& error) {
-		m_error = error;
+		m_error = "Failure to calculate particle energy loss. Reason: " + error + " See KinematicsExceptions.h for documentation.";
 	}
 
 	std::string m_error;
 
 	const char* what() const noexcept {
-		std::string err_str = "Failure to calculate particle energy loss. Reason: ";
-		err_str += m_error + " See KinematicsExceptions.h for documentation.";
-		return err_str.c_str();
+		return m_error.c_str();
 	};
 };
 
diff --git a/input.txt b/input.txt
index 9022e7a..9c11870 100644
--- a/input.txt
+++ b/input.txt
@@ -8,15 +8,14 @@ Z	A (order is target, projectile, ejectile, break1, break3(if pure decay is targ
 1	1
 2   4
 ----------Target Information----------
-Name: test_targ
-Layers: 1
-~Layer1
-Thickness(ug/cm^2): 50
-Z	A	Stoich
-1	2	2
-6	12	1
-0
-~
+NumberOfLayers: 2
+begin_layer
+	Thickness(ug/cm^2): 50
+	begin_elements (Z, A, Stoich.)
+		element	1 2 2
+		element	6 12 1
+	end_elements
+end_layer
 ----------Sampling Information----------
 NumberOfSamples: 100000
 BeamMeanEnergy(MeV): 0.87 BeamEnergySigma(MeV): 0.0
diff --git a/src/EnergyLoss.cpp b/src/EnergyLoss.cpp
index 7130849..236bb41 100644
--- a/src/EnergyLoss.cpp
+++ b/src/EnergyLoss.cpp
@@ -49,6 +49,9 @@ namespace Mask {
 			AP = ap;
 			MP = MassLookup::GetInstance().FindMass(ZP, AP)*MEV2U;
 		}
+
+		if(thickness == 0.0 || e_initial == 0.0)
+			return 0;
 	
 		double e_final = e_initial;
 		double x_traversed = 0;
@@ -58,10 +61,6 @@ namespace Mask {
 	
 		int depth=0;
 	
-		
-		if(thickness == 0.0 || e_initial == 0.0) 
-			return 0;
-	
 		bool go = true;
 		while(go) {
 			//If intial guess of step size is too large, shrink until in range
@@ -99,7 +98,7 @@ namespace Mask {
 			MP = MassLookup::GetInstance().FindMass(ZP, AP)*MEV2U;
 
 		}
-	
+
 		double e_initial = e_final;
 		double x_traversed = 0.0;
 		double x_step = 0.25*thickness; //initial step in x
diff --git a/src/MaskApp.cpp b/src/MaskApp.cpp
index d75f78e..261439f 100644
--- a/src/MaskApp.cpp
+++ b/src/MaskApp.cpp
@@ -93,17 +93,21 @@ namespace Mask {
 		double thickness;
 		getline(input, junk);
 		getline(input, junk);
-		input>>junk>>junk;
 		input>>junk>>nlayers;
 		for(int i=0; i<nlayers; i++) 
 		{
 			input>>junk>>junk>>thickness;
-			getline(input, junk);
-			getline(input, junk);
 			avec.clear(); zvec.clear(); svec.clear();
-			while(input>>z) {
-				if(z == 0) break;
-				input>>a>>s;
+			while(input>>junk) 
+			{
+				if(junk == "begin_elements")
+				{
+					input>>junk>>junk>>junk;
+					continue;
+				} 
+				else if (junk == "end_elements")
+					break;
+				input>>z>>a>>s;
 				zvec.push_back(z); avec.push_back(a); svec.push_back(s);
 			}
 			sys->AddTargetLayer(zvec, avec, svec, thickness);