Randomized energy fix

new file:   ELoss/Eloss_17F
	new file:   ELoss/Eloss_27Al
	new file:   ELoss/Eloss_alpha
	new file:   ELoss/Eloss_p
	modified:   MakeVertex.C
	deleted:    MakeVertex.C:Zone.Identifier
	deleted:    MakeVertex.h:Zone.Identifier

.gitignore

@@ -4,9 +4,29 @@ EventBuilder*
 *.pcm
 *.root
 *.exe
-
+*.txt
+*.err
+*.seq
+*.png
+*.pdf
+*.keras
 Mapper
 AnasenMS
+Armory/anasenMS
 
 data/
 data_proton/
+Sudarshan/
+Analyzer_C_ACLiC_dict0713aaa966_dictContent.h
+.gitignore
+Analyzer_C_ACLiC_dict5411fecd5c_dictUmbrella.h
+gainmatch.C
+gainmatch.h
+MakePlotsQQQ.C
+MakePlotsQQQ.h
+MakePlotsSX3.C
+MakePlotsSX3.h
+qqq_gains_det3.dat
+qqq_relative_gains.dat
+Armory/CorrelateQQQ.h
+QQQStage2.C

.vscode/c_cpp_properties.json

@@ -1,23 +1,24 @@
 {
     "configurations": [
         {
-            "name": "splitpole",
+            "name": "Linux",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/splitpole/cern/root/**"
+                "/opt/root-6.36.06/include",
+                "/home/jamesszalkie/anasen/Armory"
             ],
             "defines": [],
-            "compilerPath": "/usr/bin/gcc",
-            "cStandard": "c17",
-            "cppStandard": "gnu++17",
-            "intelliSenseMode": "linux-gcc-x64"
+            "compilerPath": "/usr/bin/g++",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "gcc-x64"
         },
         {
-            "name": "Ryan",
+            "name": "Hades",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/ryan/Downloads/root_build/**",
-                "/home/ryan/Downloads/root_build/include"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/usr/local/cern/root_v6.26.06/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -29,7 +30,8 @@
             "name": "RyanUbuntu",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -38,10 +40,11 @@
             "intelliSenseMode": "linux-gcc-x64"
         },
         {
-            "name": "RyanHome",
+            "name": "Anasen",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/ryan/root_v6.30.06/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -50,10 +53,38 @@
             "intelliSenseMode": "linux-gcc-x64"
         },
         {
-            "name": "Dirac",
+            "name": "Splitpole",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/usr/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/home/splitpole/cern/root/include/**",
+                "/usr/include/x86_64-linux-gnu/qt6/QtWidgets",
+                "/usr/include/x86_64-linux-gnu/qt6/QtCore"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "Penguin",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/usr/local/cern/root/include/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "VigneshROG",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/home/vsitaraman/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",

.vscode/settings.json

@@ -90,6 +90,42 @@
     "processRun.C": "cpp",
     "TrackRecon.C": "cpp",
     "processRuns.C": "cpp",
-    "Analysis.C": "cpp"
-  }
+    "Analysis.C": "cpp",
+    "datastructs.h": "c",
+    "ANASENPlotEdit.C": "cpp",
+    "GetMean_Q3_new.C": "cpp",
+    "AlphaCal_new.C": "cpp",
+    "f1.C": "cpp",
+    "GeoCal_Maria_new.C": "cpp",
+    "PCPulser_All_new.C": "cpp",
+    "PosCal_2.C": "cpp",
+    "AutoFit.C": "cpp",
+    "Fitting.C": "cpp",
+    "PCGainMatch.C": "cpp",
+    "Analyzer1.C": "cpp",
+    "FitHistogramsWithTSpectrum_Sequential_Improved.C": "cpp",
+    "PlotAndFitCentroids.C": "cpp",
+    "MatchAndPlotCentroids.C": "cpp",
+    "GainMatch.C": "cpp",
+    "GainMatchSX3.C": "cpp",
+    "RelBack_Fix_new.C": "cpp",
+    "SiRelativeGains_Step1_new.C": "cpp",
+    "charconv": "cpp",
+    "format": "cpp",
+    "GainMatchSX3Front.C": "cpp",
+    "GainMatchSX3Front1.C": "cpp",
+    "Calibration.C": "cpp",
+    "GainMatchQQQ.C": "cpp",
+    "UTF-8gainmatch.C": "cpp",
+    "MakePlotsQQQ.C": "cpp",
+    "MakePlotsSX3.C": "cpp",
+    "QQQ_Calibcheck.C": "cpp",
+    "QQQ_Calcheck.C": "cpp",
+    "makeplots.C": "cpp",
+    "GlobalMinimizeQQQ.C": "cpp",
+    "QQQStage2.C": "cpp",
+    "inspect.C": "cpp"
+  },
+  "github-enterprise.uri": "https://fsunuc.physics.fsu.edu",
+  "C_Cpp.default.compilerPath": "/usr/bin/gcc"
 }

Analyzer.h

@@ -18,6 +18,7 @@ public :
    Det sx3;
    Det qqq;
    Det pc ;
+   Det misc;
 
    ULong64_t       evID;
    UInt_t          run;
@@ -40,6 +41,13 @@ public :
    TBranch        *b_pcCh;   //!
    TBranch        *b_pcE;   //!
    TBranch        *b_pcT;   //!
+   TBranch        *b_miscMulti;   //!
+   TBranch        *b_miscID;   //!
+   TBranch        *b_miscCh;   //!
+   TBranch        *b_miscE;   //!
+   TBranch        *b_miscT;   //!
+   TBranch       *b_miscTf;   //!
+
 
    Analyzer(TTree * /*tree*/ =0) : fChain(0) { }
    virtual ~Analyzer() { }
@@ -92,6 +100,13 @@ void Analyzer::Init(TTree *tree){
    fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
    fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
    fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID",    &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh",    &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE",     &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT",     &misc.t, &b_miscT);
+   // fChain->SetBranchAddress("miscF",     &misc.tf, &b_miscTf);
+
 
 }
 

Analyzer1.C

@@ -0,0 +1,402 @@
+#define Analyzer1_cxx
+
+#include "Analyzer1.h"
+#include <TH2.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+
+#include <utility>
+#include <algorithm>
+
+#include "Armory/ClassSX3.h"
+#include "Armory/ClassPW.h"
+
+#include "TVector3.h"
+
+TH2F * hsx3IndexVE;
+TH2F * hqqqIndexVE;
+TH2F * hpcIndexVE;
+
+TH2F * hsx3Coin;
+TH2F * hqqqCoin;
+TH2F * hpcCoin;
+
+TH2F * hqqqPolar;
+TH2F * hsx3VpcIndex;
+TH2F * hqqqVpcIndex;
+TH2F * hqqqVpcE;
+TH2F * hsx3VpcE;
+TH2F * hanVScatsum;
+int padID = 0;
+
+SX3 sx3_contr;
+PW pw_contr;
+TVector3 hitPos;
+bool HitNonZero;
+
+TH1F * hZProj;
+
+void Analyzer1::Begin(TTree * /*tree*/){
+  TString option = GetOption();
+
+  hsx3IndexVE = new TH2F("hsx3IndexVE", "SX3 index vs Energy; sx3 index ; Energy",  24*12, 0,  24*12, 400, 0, 5000); hsx3IndexVE->SetNdivisions( -612, "x");
+  hqqqIndexVE = new TH2F("hqqqIndexVE", "QQQ index vs Energy; QQQ index ; Energy", 4*2*16, 0, 4*2*16, 400, 0, 5000); hqqqIndexVE->SetNdivisions( -1204, "x");
+  hpcIndexVE = new TH2F("hpcIndexVE",   "PC index vs Energy; PC index ; Energy",     2*24, 0,   2*24, 400, 0, 4000); hpcIndexVE->SetNdivisions( -1204, "x");
+
+
+  hsx3Coin = new TH2F("hsx3Coin", "SX3 Coincident",  24*12, 0,  24*12,  24*12, 0, 24*12);
+  hqqqCoin = new TH2F("hqqqCoin", "QQQ Coincident", 4*2*16, 0, 4*2*16, 4*2*16, 0, 4*2*16);
+  hpcCoin  = new TH2F("hpcCoin",  "PC Coincident",    2*24, 0,   2*24,   2*24, 0, 2*24);
+
+  hqqqPolar = new TH2F("hqqqPolar", "QQQ Polar ID", 16*4, -TMath::Pi(), TMath::Pi(),16, 10, 50);
+
+  hsx3VpcIndex = new TH2F("hsx3Vpcindex", "sx3 vs pc; sx3 index; pc index",  24*12, 0, 24*12, 48, 0, 48);
+  hsx3VpcIndex->SetNdivisions( -612, "x");
+  hsx3VpcIndex->SetNdivisions( -12, "y");
+  hqqqVpcIndex = new TH2F("hqqqVpcindex", "qqq vs pc; qqq index; pc index",  4*2*16, 0, 4*2*16, 48, 0, 48);
+  hqqqVpcIndex->SetNdivisions( -612, "x");
+  hqqqVpcIndex->SetNdivisions( -12, "y");
+
+  hqqqVpcE = new TH2F("hqqqVpcEnergy", "qqq vs pc; qqq energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hqqqVpcE->SetNdivisions( -612, "x");
+  hqqqVpcE->SetNdivisions( -12, "y");
+  
+  hsx3VpcE = new TH2F("hsx3VpcEnergy", "sx3 vs pc; sx3 energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hsx3VpcE->SetNdivisions( -612, "x");
+  hsx3VpcE->SetNdivisions( -12, "y");
+
+  hZProj = new TH1F("hZProj", "Z Projection", 1200, -600, 600);
+
+  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 10000, 400, 0 , 16000);
+
+  sx3_contr.ConstructGeo();
+  pw_contr.ConstructGeo();
+
+}
+
+
+
+
+Bool_t Analyzer1::Process(Long64_t entry){
+
+  // if ( entry > 100 ) return kTRUE;
+
+  hitPos.Clear();
+  HitNonZero = false;
+
+  // if( entry > 1) return kTRUE;
+  // printf("################### ev : %llu \n", entry);
+
+  b_sx3Multi->GetEntry(entry);
+  b_sx3ID->GetEntry(entry);
+  b_sx3Ch->GetEntry(entry);
+  b_sx3E->GetEntry(entry);
+  b_sx3T->GetEntry(entry);
+  b_qqqMulti->GetEntry(entry);
+  b_qqqID->GetEntry(entry);
+  b_qqqCh->GetEntry(entry);
+  b_qqqE->GetEntry(entry);
+  b_qqqT->GetEntry(entry);
+  b_pcMulti->GetEntry(entry);
+  b_pcID->GetEntry(entry);
+  b_pcCh->GetEntry(entry);
+  b_pcE->GetEntry(entry);
+  b_pcT->GetEntry(entry);
+
+  sx3.CalIndex();
+  qqq.CalIndex();
+  pc.CalIndex();
+
+  // sx3.Print();
+
+  //########################################################### Raw data
+  // //======================= SX3
+
+  std::vector<std::pair<int, int>> ID; // first = id, 2nd = index
+  for( int i = 0; i < sx3.multi; i ++){
+    ID.push_back(std::pair<int, int>(sx3.id[i], i));
+
+    hsx3IndexVE->Fill( sx3.index[i], sx3.e[i] );
+
+    for( int j = i+1; j < sx3.multi; j++){
+      hsx3Coin->Fill( sx3.index[i], sx3.index[j]);
+    }
+
+    for( int j = 0; j < pc.multi; j++){
+      hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+      //  if( sx3.ch[index] > 8 ){
+      //    hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+      //   }
+    }
+  }
+
+
+  if( ID.size() > 0 ){
+    std::sort(ID.begin(), ID.end(),  [](const std::pair<int, int> & a, const std::pair<int, int> & b) {
+      return a.first < b.first;
+    } );
+    // printf("##############################\n");
+    // for( size_t i = 0; i < ID.size(); i++) printf("%zu | %d %d \n", i, ID[i].first, ID[i].second );
+
+    std::vector<std::pair<int, int>> sx3ID; 
+    sx3ID.push_back(ID[0]);
+    bool found = false;
+    for( size_t i = 1; i < ID.size(); i++){
+      if( ID[i].first == sx3ID.back().first) {
+        sx3ID.push_back(ID[i]);
+        if( sx3ID.size() >= 3) {
+          found = true;
+        } 
+      }else{
+        if( !found ){
+          sx3ID.clear();
+          sx3ID.push_back(ID[i]);
+        }
+      }
+    }
+
+    // printf("---------- sx3ID Multi : %zu \n", sx3ID.size());
+
+    if( found ){
+      int sx3ChUp, sx3ChDn, sx3ChBk;
+      float sx3EUp, sx3EDn;
+      // printf("------ sx3 ID : %d, multi: %zu\n", sx3ID[0].first, sx3ID.size());
+      for( size_t i = 0; i < sx3ID.size(); i++ ){
+        int index = sx3ID[i].second;
+        // printf(" %zu | index %d | ch : %d, energy : %d \n", i, index, sx3.ch[index], sx3.e[index]);
+
+
+        if( sx3.ch[index] < 8 ){
+          if( sx3.ch[index] % 2 == 0) {
+            sx3ChDn = sx3.ch[index];
+            sx3EDn = sx3.e[index];
+          }else{
+            sx3ChUp = sx3.ch[index];
+            sx3EUp = sx3.e[index];
+          }
+        }else{
+          sx3ChBk = sx3.ch[index];
+        }
+         for( int j = 0; j < pc.multi; j++){
+      // hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+            if( sx3.ch[index] > 8 ){
+              hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+            }
+          }
+      }
+
+      sx3_contr.CalSX3Pos(sx3ID[0].first, sx3ChUp, sx3ChDn, sx3ChBk, sx3EUp, sx3EDn);
+      hitPos = sx3_contr.GetHitPos();
+      HitNonZero = true;
+      // hitPos.Print();
+    }
+
+  }
+  
+
+  // //======================= QQQ
+  for( int i = 0; i < qqq.multi; i ++){
+    // for( int j = 0; j < pc.multi; j++){
+        // if(pc.index[j]==4){
+          hqqqIndexVE->Fill( qqq.index[i], qqq.e[i] );
+        // }
+    // }
+    for( int j = 0; j < qqq.multi; j++){
+      if ( j == i ) continue;
+      hqqqCoin->Fill( qqq.index[i], qqq.index[j]);
+    }
+
+
+    for( int j = i + 1; j < qqq.multi; j++){
+      for( int k = 0; k < pc.multi; k++){
+        if(pc.index[k]<24 && pc.e[k]>50 ){
+          hqqqVpcE->Fill( qqq.e[i], pc.e[k] );
+          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+                hqqqVpcIndex->Fill( qqq.index[i], pc.index[j] );
+
+        }
+      // }
+      }
+      // if( qqq.used[i] == true ) continue;
+      
+      //if( qqq.id[i] == qqq.id[j] && (16 - qqq.ch[i]) * (16 - qqq.ch[j]) < 0  ){ // must be same detector and wedge and ring
+      if( qqq.id[i] == qqq.id[j]  ){ // must be same detector 
+        
+        int chWedge = -1;
+        int chRing  =  -1;
+        if( qqq.ch[i] < qqq.ch[j]){
+          chRing = qqq.ch[j] - 16;
+          chWedge = qqq.ch[i];
+        }else{
+          chRing = qqq.ch[i];
+          chWedge = qqq.ch[j] - 16;
+        }
+
+        // printf(" ID : %d , chWedge : %d, chRing : %d \n", qqq.id[i], chWedge, chRing);
+
+        double theta = -TMath::Pi()/2 + 2*TMath::Pi()/16/4.*(qqq.id[i]*16 + chWedge +0.5);
+        double rho   = 10.+40./16.*(chRing+0.5);
+        // if(qqq.e[i]>50){
+        hqqqPolar->Fill( theta, rho);
+        // }
+        // qqq.used[i] = true;
+        // qqq.used[j] = true;
+
+        if( !HitNonZero ){
+        double x = rho * TMath::Cos(theta);
+        double y = rho * TMath::Sin(theta);
+        hitPos.SetXYZ(x, y, 23 + 75 + 30);
+        HitNonZero = true;
+        }
+      }
+    }
+  
+   
+  }
+  // //======================= PC
+
+  ID.clear();
+  int counter=0;
+  std::vector<std::pair<int, double>> E; 
+  E.clear();
+  for( int i = 0; i < pc.multi; i ++){
+
+    if( pc.e[i] > 100 ) ID.push_back(std::pair<int, int>(pc.id[i], i));
+    if( pc.e[i] > 100 ) E.push_back(std::pair<int, double>(pc.index[i], pc.e[i]));
+
+    hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+
+    for( int j = i+1; j < pc.multi; j++){
+      hpcCoin->Fill( pc.index[i], pc.index[j]);
+    
+    }
+
+  }
+  //  for( size_t i = 0; i < E.size(); i++) printf("%zu | %d %d \n", i, E[i].first, E[i].second ); 
+
+  if( E.size()>=3 ){
+
+    int aID = 0;
+    int cID = 0;
+
+    float aE = 0;
+    float cE = 0;
+    bool multi_an =false;
+    // if( ID[0].first < 1 ) {
+    //   aID = pc.ch[ID[0].second];
+    //   cID = pc.ch[ID[1].second];
+    // }else{
+    //   cID = pc.ch[ID[0].second];
+    //   aID = pc.ch[ID[1].second];
+    // }
+    // printf("anode= %d, cathode = %d\n", aID, cID);
+
+  // for( int k = 0; k < qqq.multi; k++){
+  //   if(qqq.index[k]==75 && pc.index[k]==2 && pc.e[k]>100){
+      for(int l=0;l<E.size();l++){
+        if(E[l].first<24 ){
+          if(!multi_an){
+            aE = E[l].second;
+          }
+          multi_an=true;
+        }
+        else if (E[l].first>=24){
+          cE = E[l].second + cE;
+        }
+      }
+    // }
+  // }
+    hanVScatsum->Fill(aE,cE);
+      
+    if( ID[0].first < 1 ) {
+      aID = pc.ch[ID[0].second];
+      cID = pc.ch[ID[1].second];
+    }else{
+      cID = pc.ch[ID[0].second];
+      aID = pc.ch[ID[1].second];
+    }
+
+    if( HitNonZero){
+      pw_contr.CalTrack( hitPos, aID, cID);
+      hZProj->Fill(pw_contr.GetZ0());
+    }
+
+  
+  }
+  
+
+
+  //########################################################### Track constrcution
+
+
+  //############################## DO THE KINEMATICS
+
+
+  return kTRUE;
+}
+
+void Analyzer1::Terminate(){
+
+  gStyle->SetOptStat("neiou");
+  TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
+  canvas->Divide(3,3);
+
+  //hsx3VpcIndex->Draw("colz");
+
+  //=============================================== pad-1
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3IndexVE->Draw("colz");
+
+  //=============================================== pad-2
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hqqqIndexVE->Draw("colz");
+
+  //=============================================== pad-3
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcIndexVE->Draw("colz");
+
+  //=============================================== pad-4
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3Coin->Draw("colz");
+
+  //=============================================== pad-5
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  canvas->cd(padID)->SetLogz(true);
+
+  hqqqCoin->Draw("colz");
+
+  //=============================================== pad-6
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcCoin->Draw("colz");
+
+  //=============================================== pad-7
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hsx3VpcIndex ->Draw("colz"); 
+  hsx3VpcE->Draw("colz") ;
+
+  //=============================================== pad-8
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hqqqVpcIndex ->Draw("colz");  
+
+  hqqqVpcE ->Draw("colz");
+  //=============================================== pad-9
+  padID ++; 
+
+  // canvas->cd(padID)->DrawFrame(-50, -50, 50, 50);
+  // hqqqPolar->Draw("same colz pol");
+
+ canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+//  hZProj->Draw();
+  hanVScatsum->Draw("colz");
+
+}

Analyzer1.h

@@ -0,0 +1,114 @@
+#ifndef Analyzer1_h
+#define Analyzer1_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class Analyzer1 : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   Analyzer1(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~Analyzer1() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(Analyzer1,0);
+};
+
+#endif
+
+#ifdef Analyzer1_cxx
+void Analyzer1::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t Analyzer1::Notify(){
+
+   return kTRUE;
+}
+
+void Analyzer1::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void Analyzer1::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef Analyzer_cxx

Armory/ANASEN_ML.py

@@ -0,0 +1,178 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Aug  5 15:52:39 2026
+
+@author: jamesszalkie
+"""
+
+import uproot
+import joblib
+import numpy as np
+import matplotlib.pyplot as plt
+import tensorflow as tf
+from sklearn.metrics import mean_absolute_error
+
+# User settings
+
+ROOT_FILE = "/Users/jamesszalkie/ANASEN_analysis/Armory/SimAnasen1.root"
+TREE_NAME = "tree1"
+
+MODEL = "beam_predictor.keras"
+INPUT_SCALER = "input_scaler.pkl"
+OUTPUT_SCALER = "output_scaler.pkl"
+
+INPUT_BRANCHES = [
+    "Tb",
+    "thetab",
+    "vZ",
+    "MBeam",
+    "MTarget",
+    "MLight",
+    "MHeavy",
+]
+
+# Load model
+
+model = tf.keras.models.load_model(MODEL)
+
+input_scaler = joblib.load(INPUT_SCALER)
+output_scaler = joblib.load(OUTPUT_SCALER)
+
+# Read ROOT file
+
+with uproot.open(ROOT_FILE) as f:
+    tree = f[TREE_NAME]
+    arrays = tree.arrays(INPUT_BRANCHES, library="np")
+
+X = np.column_stack([arrays[b] for b in INPUT_BRANCHES])
+
+# Remove NaN events
+mask = np.all(np.isfinite(X), axis=1)
+X = X[mask]
+
+print(f"Predicting {len(X)} events")
+
+# Predict
+
+X_scaled = input_scaler.transform(X)
+
+pred_scaled = model.predict(X_scaled, verbose=0)
+
+pred = output_scaler.inverse_transform(pred_scaled)
+
+beam = pred[:,0]
+Ex = pred[:,1]
+
+# See whether truth branches exist
+
+truth_beam = None
+truth_Ex = None
+
+with uproot.open(ROOT_FILE) as f:
+
+    tree = f[TREE_NAME]
+    branches = tree.keys()
+
+    if "beamEnergy" in branches:
+        truth_beam = tree["beamEnergy"].array(library="np")[mask]
+
+    if "Ex" in branches:
+        truth_Ex = tree["Ex"].array(library="np")[mask]
+        
+print("\n============================")
+print("Model Performance")
+print("============================")
+
+if truth_beam is not None:
+    beam_mae = mean_absolute_error(truth_beam, beam)
+    beam_rmse = np.sqrt(np.mean((truth_beam - beam)**2))
+
+    print(f"Beam Energy MAE : {beam_mae:.4f} MeV")
+    print(f"Beam Energy RMSE: {beam_rmse:.4f} MeV")
+
+if truth_Ex is not None:
+    Ex_mae = mean_absolute_error(truth_Ex, Ex)
+    Ex_rmse = np.sqrt(np.mean((truth_Ex - Ex)**2))
+
+    print(f"Excitation MAE  : {Ex_mae:.4f} MeV")
+    print(f"Excitation RMSE : {Ex_rmse:.4f} MeV")
+
+# Plot Beam Energy
+plt.figure(figsize=(8,6))
+
+plt.hist(
+    beam,
+    bins=250,
+    histtype="step",
+    linewidth=2,
+    label="Predicted",
+)
+
+if truth_beam is not None:
+    plt.hist(
+        truth_beam,
+        bins=250,
+        histtype="step",
+        linewidth=2,
+        label="Truth",
+    )
+
+plt.xlabel("Beam Energy (MeV)")
+plt.ylabel("Counts")
+plt.title("Beam Energy")
+plt.legend()
+plt.tight_layout()
+
+# Plot Excitation Energy
+
+plt.figure(figsize=(8,6))
+
+plt.hist(
+    Ex,
+    bins=250,
+    histtype="step",
+    linewidth=2,
+    label="Predicted",
+)
+
+if truth_Ex is not None:
+    plt.hist(
+        truth_Ex,
+        bins=250,
+        histtype="step",
+        linewidth=2,
+        label="Truth",
+    )
+
+plt.xlabel("Excitation Energy (MeV)")
+plt.ylabel("Counts")
+plt.title("Excitation Energy")
+plt.legend()
+plt.tight_layout()
+
+plt.figure(figsize=(6,6))
+
+plt.scatter(truth_beam, beam, s=2)
+
+mn = min(truth_beam.min(), beam.min())
+mx = max(truth_beam.max(), beam.max())
+
+plt.plot([mn, mx], [mn, mx], 'k--')
+
+plt.xlabel("True Beam Energy (MeV)")
+plt.ylabel("Predicted Beam Energy (MeV)")
+plt.title("Beam Energy Reconstruction")
+
+plt.figure(figsize=(6,6))
+
+plt.scatter(truth_Ex, Ex, s=2)
+
+mn = min(truth_Ex.min(), Ex.min())
+mx = max(truth_Ex.max(), Ex.max())
+
+plt.plot([mn, mx], [mn, mx], 'k--')
+
+plt.xlabel("True Excitation Energy (MeV)")
+plt.ylabel("Predicted Excitation Energy (MeV)")
+plt.title("Excitation Energy Reconstruction")

Armory/ANASEN_model.C

@@ -26,23 +26,35 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
   TGeoVolume *worldBox = geom->MakeBox("ROOT", Vacuum, worldx, worldy, worldz);
   geom->SetTopVolume(worldBox);
 
-  //--- making axis
-  TGeoVolume *axisX = geom->MakeTube("axisX", Al, 0, 0.1, 5.);
-  axisX->SetLineColor(1);
-  worldBox->AddNode(axisX, 1, new TGeoCombiTrans(5, 0, 0., new TGeoRotation("rotA", 90., 90., 0.)));
+  //--- making axis (X=red, Y=green, Z=blue)
+  Double_t axisLen = 100.;
+  TGeoVolume *axisX = geom->MakeTube("axisX", Al, 0, 0.1, axisLen/2);
+  axisX->SetLineColor(kRed);
+  worldBox->AddNode(axisX, 1, new TGeoCombiTrans(axisLen/2, 0, 0., new TGeoRotation("rotA", 90., 90., 0.)));
 
-  TGeoVolume *axisY = geom->MakeTube("axisY", Al, 0, 0.1, 5.);
-  axisY->SetLineColor(1);
-  worldBox->AddNode(axisY, 1, new TGeoCombiTrans(0, 5, 0., new TGeoRotation("rotB", 0., 90., 0.)));
+  TGeoVolume *axisY = geom->MakeTube("axisY", Al, 0, 0.1, axisLen/2);
+  axisY->SetLineColor(kGreen);
+  worldBox->AddNode(axisY, 1, new TGeoCombiTrans(0, axisLen/2, 0., new TGeoRotation("rotB", 0., 90., 0.)));
 
-  TGeoVolume *axisZ = geom->MakeTube("axisZ", Al, 0, 0.1, 5.);
-  axisZ->SetLineColor(1);
-  worldBox->AddNode(axisZ, 1, new TGeoTranslation(0, 0,  5));
+  TGeoVolume *axisZ = geom->MakeTube("axisZ", Al, 0, 0.1, axisLen/2);
+  axisZ->SetLineColor(kBlue);
+  worldBox->AddNode(axisZ, 1, new TGeoTranslation(0, 0, axisLen/2));
+
+  //--- axis labels (draw as TPolyMarker3D + text because TGeo does not label directly)
+  TPolyMarker3D *marker = new TPolyMarker3D();
+  marker->SetMarkerSize(1.2);
+  marker->SetMarkerColor(kRed);
+  marker->SetPoint(0, axisLen, 0, 0); // X
+  marker->SetMarkerColor(kGreen);
+  marker->SetPoint(1, 0, axisLen, 0); // Y
+  marker->SetMarkerColor(kBlue);
+  marker->SetPoint(2, 0, 0, axisLen); // Z
+  marker->Draw();
 
   //--- making ANASEN
   const int nWire = 24;
   const int wireShift = 3;
-  const int zLen = 300; //mm
+  const int zLen = 350; //mm
   const int radiusA = 38;
   const int radiusC = 43;
 
@@ -103,8 +115,8 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
                                                        new TGeoRotation("rot1", 360/nSX3 * (i + 0.5), 0., 0.)));
   }
 
-  const int qqqR1 = 10;
-  const int qqqR2 = 50;
+  const int qqqR1 = 50;
+  const int qqqR2 = 100;
   TGeoVolume *qqq = geom->MakeTubs("qqq", Al, qqqR1, qqqR2, 0.5, 5, 85);
   qqq->SetLineColor(7);
   for( int i = 0; i < 4; i++){
@@ -119,3 +131,5 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
   geom->SetVisLevel(4);
   worldBox->Draw("ogle");
 }
+
+

Armory/AnasenG4/G4History.macro

@@ -0,0 +1,64 @@
+/run/verbose 2
+/event/verbose 0
+/tracking/verbose 0
+/run/initialize
+/control/execute vis.mac
+/vis/open
+/vis/sceneHandler/create TSG
+/vis/viewer/create ! ! 600x600-0+0
+/vis/viewer/refresh
+/vis/viewer/set/autoRefresh false
+/vis/verbose errors
+/vis/drawVolume
+/vis/scene/create
+/vis/scene/add/volume world -1 -1 none m 0 0 0 0 0 0
+/vis/sceneHandler/attach
+/vis/viewer/set/viewpointVector -1 0 0
+/vis/viewer/set/lightsVector -1 0 0
+/vis/viewer/set/style wireframe
+/vis/viewer/set/auxiliaryEdge true
+/vis/viewer/set/lineSegmentsPerCircle 100
+/tracking/storeTrajectory 1
+/vis/scene/add/trajectories smooth
+/tracking/storeTrajectory 2
+/vis/scene/notifyHandlers
+/vis/modeling/trajectories/create/drawByParticleID
+/vis/modeling/trajectories/drawByParticleID-0/default/setDrawStepPts true
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByParticleID-0/default/setStepPtsSize 2
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByParticleID-0/set proton magenta
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByParticleID-0/set alpha orange
+/vis/scene/notifyHandlers scene-0
+/vis/scene/endOfEventAction accumulate 20
+/vis/geometry/set/visibility World 0 false
+/vis/scene/notifyHandlers
+/vis/scene/add/axes 0 0 0 20 mm
+/vis/scene/notifyHandlers
+/vis/viewer/set/background 0 0 0
+/vis/viewer/set/style surface
+/vis/viewer/set/hiddenMarker true
+/vis/viewer/set/viewpointThetaPhi 120 150
+/vis/viewer/set/autoRefresh true
+/vis/viewer/refresh
+/vis/verbose warnings
+/vis/viewer/flush
+/vis/viewer/refresh viewer-0
+/vis/viewer/update viewer-0
+/control/execute run.mac
+/control/verbose 1
+/run/verbose 1
+/event/verbose 0
+/tracking/verbose 0
+/anasen/output/includeElectrons false
+/run/initialize
+/vis/filtering/trajectories/create/particleFilter
+/vis/filtering/trajectories/particleFilter-0/add e-
+/vis/scene/notifyHandlers scene-0
+/vis/filtering/trajectories/particleFilter-0/add e+
+/vis/scene/notifyHandlers scene-0
+/vis/filtering/trajectories/particleFilter-0/invert true
+/vis/scene/notifyHandlers scene-0
+/run/beamOn 1000
+/vis/scene/notifyHandlers scene-0

Armory/AnasenG4/README.md

@@ -0,0 +1,34 @@
+# AnasenG4 Geant4 Simulation
+
+This folder contains a minimal Geant4 application that: 
+- builds the ANASEN detector geometry,
+- adds a helium target volume,
+- generates outgoing proton events from an `18Ne + 4He` alpha/p reaction using the external `ClassTransfer` reaction model,
+- and propagates the particles with the Geant4 `FTFP_BERT` physics list.
+
+## Build
+
+```bash
+cd /home/jamesszalkie/anasen/Armory/AnasenG4
+rm -rf build
+mkdir build
+cd build
+cmake ..
+make -j4
+```
+
+## Run
+
+```bash
+cd /home/jamesszalkie/anasen/Armory/AnasenG4
+./build/AnasenG4 macros/run.mac
+```
+
+## Notes
+
+- The reaction generator uses `/home/jamesszalkie/anasen/Armory/mass20.txt` for isotope mass lookups.
+- You can also run the interactive visualization macro:
+
+```bash
+./build/AnasenG4 macros/init_vis.mac
+```

Armory/AnasenG4/build/CMakeFiles/3.22.1/CMakeCXXCompiler.cmake

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+
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+src/WireTrackingManager.i: src/WireTrackingManager.cc.i
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+
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+
+# target to generate assembly for a file
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+.PHONY : src/WireTrackingManager.cc.s
+
+src/main.o: src/main.cc.o
+.PHONY : src/main.o
+
+# target to build an object file
+src/main.cc.o:
+	$(MAKE) $(MAKESILENT) -f CMakeFiles/AnasenG4.dir/build.make CMakeFiles/AnasenG4.dir/src/main.cc.o
+.PHONY : src/main.cc.o
+
+src/main.i: src/main.cc.i
+.PHONY : src/main.i
+
+# target to preprocess a source file
+src/main.cc.i:
+	$(MAKE) $(MAKESILENT) -f CMakeFiles/AnasenG4.dir/build.make CMakeFiles/AnasenG4.dir/src/main.cc.i
+.PHONY : src/main.cc.i
+
+src/main.s: src/main.cc.s
+.PHONY : src/main.s
+
+# target to generate assembly for a file
+src/main.cc.s:
+	$(MAKE) $(MAKESILENT) -f CMakeFiles/AnasenG4.dir/build.make CMakeFiles/AnasenG4.dir/src/main.cc.s
+.PHONY : src/main.cc.s
+
+# Help Target
+help:
+	@echo "The following are some of the valid targets for this Makefile:"
+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... edit_cache"
+	@echo "... rebuild_cache"
+	@echo "... AnasenG4"
+	@echo "... src/ActionInitialization.o"
+	@echo "... src/ActionInitialization.i"
+	@echo "... src/ActionInitialization.s"
+	@echo "... src/BeamReactionSteppingAction.o"
+	@echo "... src/BeamReactionSteppingAction.i"
+	@echo "... src/BeamReactionSteppingAction.s"
+	@echo "... src/DetectorConstruction.o"
+	@echo "... src/DetectorConstruction.i"
+	@echo "... src/DetectorConstruction.s"
+	@echo "... src/DetectorSensitiveDetector.o"
+	@echo "... src/DetectorSensitiveDetector.i"
+	@echo "... src/DetectorSensitiveDetector.s"
+	@echo "... src/HitOutputManager.o"
+	@echo "... src/HitOutputManager.i"
+	@echo "... src/HitOutputManager.s"
+	@echo "... src/PrimaryGeneratorAction.o"
+	@echo "... src/PrimaryGeneratorAction.i"
+	@echo "... src/PrimaryGeneratorAction.s"
+	@echo "... src/ReactionGenerator.o"
+	@echo "... src/ReactionGenerator.i"
+	@echo "... src/ReactionGenerator.s"
+	@echo "... src/RunAction.o"
+	@echo "... src/RunAction.i"
+	@echo "... src/RunAction.s"
+	@echo "... src/WireTrackingManager.o"
+	@echo "... src/WireTrackingManager.i"
+	@echo "... src/WireTrackingManager.s"
+	@echo "... src/main.o"
+	@echo "... src/main.i"
+	@echo "... src/main.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+	$(CMAKE_COMMAND) -S$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+

Armory/AnasenG4/build/cmake_install.cmake

@@ -0,0 +1,54 @@
+# Install script for directory: /home/jamesszalkie/anasen/Armory/AnasenG4
+
+# Set the install prefix
+if(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  set(CMAKE_INSTALL_PREFIX "/usr/local")
+endif()
+string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  if(BUILD_TYPE)
+    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  else()
+    set(CMAKE_INSTALL_CONFIG_NAME "")
+  endif()
+  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+endif()
+
+# Set the component getting installed.
+if(NOT CMAKE_INSTALL_COMPONENT)
+  if(COMPONENT)
+    message(STATUS "Install component: \"${COMPONENT}\"")
+    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  else()
+    set(CMAKE_INSTALL_COMPONENT)
+  endif()
+endif()
+
+# Install shared libraries without execute permission?
+if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+  set(CMAKE_INSTALL_SO_NO_EXE "1")
+endif()
+
+# Is this installation the result of a crosscompile?
+if(NOT DEFINED CMAKE_CROSSCOMPILING)
+  set(CMAKE_CROSSCOMPILING "FALSE")
+endif()
+
+# Set default install directory permissions.
+if(NOT DEFINED CMAKE_OBJDUMP)
+  set(CMAKE_OBJDUMP "/usr/bin/objdump")
+endif()
+
+if(CMAKE_INSTALL_COMPONENT)
+  set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
+else()
+  set(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
+endif()
+
+string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
+       "${CMAKE_INSTALL_MANIFEST_FILES}")
+file(WRITE "/home/jamesszalkie/anasen/Armory/AnasenG4/build/${CMAKE_INSTALL_MANIFEST}"
+     "${CMAKE_INSTALL_MANIFEST_CONTENT}")

Armory/AnasenG4/include/ActionInitialization.hh

@@ -0,0 +1,15 @@
+#ifndef ActionInitialization_h
+#define ActionInitialization_h 1
+
+#include "G4VUserActionInitialization.hh"
+
+class ActionInitialization : public G4VUserActionInitialization
+{
+  public:
+    ActionInitialization();
+    virtual ~ActionInitialization();
+
+    virtual void Build() const override;
+};
+
+#endif

Armory/AnasenG4/include/BeamConfig.hh

@@ -0,0 +1,17 @@
+#ifndef BeamConfig_h
+#define BeamConfig_h 1
+
+#include "globals.hh"
+#include "G4SystemOfUnits.hh"
+
+namespace BeamConfig {
+inline constexpr G4int kAtomicNumber = 13;
+inline constexpr G4int kAtomicMass = 27;
+inline constexpr G4double kRadius = 5.0 * mm;
+inline constexpr G4double kStartZ = -190.0 * mm;
+inline constexpr G4double kTotalBeamEnergy = 72.0 * MeV;
+inline constexpr G4double kEnergyPerU = kTotalBeamEnergy / kAtomicMass; // Approximately 2.67 MeV/u for 27Al
+inline constexpr char kTargetVolumeName[] = "Target";
+}  // namespace BeamConfig
+
+#endif

Armory/AnasenG4/include/BeamReactionSteppingAction.hh

@@ -0,0 +1,21 @@
+#ifndef BeamReactionSteppingAction_h
+#define BeamReactionSteppingAction_h 1
+
+#include "G4UserSteppingAction.hh"
+
+class G4Step;
+class ReactionGenerator;
+
+class BeamReactionSteppingAction : public G4UserSteppingAction
+{
+  public:
+    BeamReactionSteppingAction();
+    virtual ~BeamReactionSteppingAction();
+
+    virtual void UserSteppingAction(const G4Step* step) override;
+
+  private:
+    ReactionGenerator* fReaction;
+};
+
+#endif

Armory/AnasenG4/include/DetectorConstruction.hh

@@ -0,0 +1,27 @@
+#ifndef DetectorConstruction_h
+#define DetectorConstruction_h 1
+
+#include "G4VUserDetectorConstruction.hh"
+
+class G4LogicalVolume;
+
+class DetectorConstruction : public G4VUserDetectorConstruction
+{
+  public:
+    DetectorConstruction();
+    virtual ~DetectorConstruction();
+
+    virtual G4VPhysicalVolume* Construct() override;
+    virtual void ConstructSDandField() override;
+
+    G4LogicalVolume* GetScoringVolume() const { return fScoringVolume; }
+
+  private:
+    G4LogicalVolume* fScoringVolume;
+    G4LogicalVolume* fAnodeLogical;
+    G4LogicalVolume* fCathodeLogical;
+    G4LogicalVolume* fSX3Logical;
+    G4LogicalVolume* fQQQLogical;
+};
+
+#endif

Armory/AnasenG4/include/DetectorSensitiveDetector.hh

@@ -0,0 +1,18 @@
+#ifndef DetectorSensitiveDetector_h
+#define DetectorSensitiveDetector_h 1
+
+#include "G4VSensitiveDetector.hh"
+
+class G4Step;
+class G4TouchableHistory;
+
+class DetectorSensitiveDetector : public G4VSensitiveDetector
+{
+  public:
+    explicit DetectorSensitiveDetector(const G4String& name);
+    virtual ~DetectorSensitiveDetector();
+
+    virtual G4bool ProcessHits(G4Step* step, G4TouchableHistory* history) override;
+};
+
+#endif

Armory/AnasenG4/include/HitOutputManager.hh

@@ -0,0 +1,83 @@
+#ifndef HitOutputManager_h
+#define HitOutputManager_h 1
+
+#include "G4ThreeVector.hh"
+
+#include <fstream>
+#include <string>
+
+class TFile;
+class TTree;
+class TH1D;
+class TH2D;
+
+class HitOutputManager
+{
+  public:
+    static HitOutputManager& Instance();
+
+    void Open();
+    void Close();
+    void SetIncludeElectrons(bool includeElectrons);
+    bool GetIncludeElectrons() const;
+    bool ShouldRecordParticle(const std::string& particleType) const;
+    void RecordHit(int eventId,
+                   const std::string& particleType,
+                   double kineticEnergy,
+                   double energyDeposit,
+                   double wireDeltaESinTheta,
+                   const std::string& detectorType,
+                   int detectorId,
+                   int anodeId,
+                   int cathodeId,
+                   double anodeEnergy,
+                   double cathodeEnergy,
+                   double wireDeltaE,
+                   const std::string& volumeName,
+                   const G4ThreeVector& position,
+                   const G4ThreeVector& vertexPosition);
+
+  private:
+    HitOutputManager();
+    ~HitOutputManager();
+
+    HitOutputManager(const HitOutputManager&) = delete;
+    HitOutputManager& operator=(const HitOutputManager&) = delete;
+
+    void ResetBuffers();
+
+    TFile* fRootFile;
+    TTree* fTree;
+    std::ofstream fTextFile;
+    int fEventId;
+    int fDetectorId;
+    int fAnodeId;
+    int fCathodeId;
+    double fKineticEnergy;
+    double fEnergyDeposit;
+    double fWireDeltaESinTheta;
+    double fAnodeEnergy;
+    double fCathodeEnergy;
+    double fWireDeltaE;
+    double fX;
+    double fY;
+    double fZ;
+    double fVertexX;
+    double fVertexY;
+    double fVertexZ;
+    char fParticleType[64];
+    char fDetectorType[32];
+    char fVolumeName[32];
+    TH1D* fKineticEnergyHist;
+    TH1D* fEnergyDepositHist;
+    TH1D* fWireDeltaEHist;
+    TH2D* fWireDeltaESinThetaVsDetEHist;
+    TH1D* fHitZHist;
+    TH1D* fVertexZHist;
+    TH1D* fDetectorIdHist;
+    TH2D* fHitXYHist;
+    TH2D* fVertexXYHist;
+    bool fIncludeElectrons;
+};
+
+#endif

Armory/AnasenG4/include/PrimaryGeneratorAction.hh

@@ -0,0 +1,24 @@
+#ifndef PrimaryGeneratorAction_h
+#define PrimaryGeneratorAction_h 1
+
+#include "G4VUserPrimaryGeneratorAction.hh"
+#include "G4ThreeVector.hh"
+
+class G4ParticleGun;
+class G4Event;
+
+class PrimaryGeneratorAction : public G4VUserPrimaryGeneratorAction
+{
+  public:
+    PrimaryGeneratorAction();
+    virtual ~PrimaryGeneratorAction();
+
+    virtual void GeneratePrimaries(G4Event* event) override;
+
+  private:
+    G4ParticleGun* fParticleGun;
+    G4double fBeamRadius;
+    G4double fBeamStartZ;
+};
+
+#endif

Armory/AnasenG4/include/ReactionGenerator.hh

@@ -0,0 +1,33 @@
+#ifndef ReactionGenerator_h
+#define ReactionGenerator_h 1
+
+#include "G4ThreeVector.hh"
+
+enum class ReactionChannel {
+  Proton,
+  Alpha
+};
+
+struct ReactionOutput {
+  ReactionChannel channel;
+  double kineticEnergy;
+  double px;
+  double py;
+  double pz;
+};
+
+class ReactionGenerator {
+ public:
+  ReactionGenerator();
+  ~ReactionGenerator();
+
+  ReactionOutput SampleEvent(double beamKineticEnergy, const G4ThreeVector& beamDirection);
+  double GetEffectiveCrossSection() const;
+
+ private:
+  class Impl;
+  Impl* fImpl;
+  double fEffectiveSigma;
+};
+
+#endif

Armory/AnasenG4/include/RunAction.hh

@@ -0,0 +1,25 @@
+#ifndef RunAction_h
+#define RunAction_h 1
+
+#include "G4UserRunAction.hh"
+
+class G4Run;
+class G4GenericMessenger;
+
+class RunAction : public G4UserRunAction
+{
+  public:
+    RunAction();
+    virtual ~RunAction();
+
+    virtual void BeginOfRunAction(const G4Run* run) override;
+    virtual void EndOfRunAction(const G4Run* run) override;
+
+  private:
+    void DefineCommands();
+
+    G4GenericMessenger* fMessenger;
+    bool fIncludeElectrons;
+};
+
+#endif

Armory/AnasenG4/include/WireTrackingManager.hh

@@ -0,0 +1,45 @@
+#ifndef WireTrackingManager_h
+#define WireTrackingManager_h 1
+
+#include "G4ThreeVector.hh"
+
+#include <unordered_map>
+
+class G4Step;
+class G4Track;
+class G4StepPoint;
+
+struct WireCrossingInfo
+{
+  int anodeId = -1;
+  int cathodeId = -1;
+  double anodeEnergy = 0.0;
+  double cathodeEnergy = 0.0;
+  double deltaE = 0.0;
+  bool sawAnode = false;
+  bool sawCathode = false;
+};
+
+class WireTrackingManager
+{
+  public:
+    static WireTrackingManager& Instance();
+
+    void UpdateForStep(const G4Step* step);
+    bool GetInfo(int eventId, int trackId, WireCrossingInfo& info);
+    WireCrossingInfo InferFromTrackGeometry(const G4Track* track, const G4StepPoint* hitPoint);
+
+  private:
+    WireTrackingManager();
+    ~WireTrackingManager();
+
+    WireTrackingManager(const WireTrackingManager&) = delete;
+    WireTrackingManager& operator=(const WireTrackingManager&) = delete;
+
+    void EnsureEvent(int eventId);
+
+    int fCurrentEventId;
+    std::unordered_map<int, WireCrossingInfo> fTrackInfo;
+};
+
+#endif

Armory/AnasenG4/init_vis.mac

@@ -0,0 +1,7 @@
+/control/verbose 2
+/control/saveHistory
+/run/verbose 2
+/event/verbose 0
+/tracking/verbose 0
+/run/initialize
+/control/execute vis.mac

Armory/AnasenG4/run.mac

@@ -0,0 +1,14 @@
+/control/verbose 1
+/run/verbose 1
+/event/verbose 0
+/tracking/verbose 0
+/anasen/output/includeElectrons false
+/run/initialize
+
+/vis/filtering/trajectories/create/particleFilter
+/vis/filtering/trajectories/particleFilter-0/add e-
+/vis/filtering/trajectories/particleFilter-0/add e+
+/vis/filtering/trajectories/particleFilter-0/invert true
+
+/run/beamOn 1000000
+#/run/beamOn 1000

Armory/AnasenG4/src/ActionInitialization.cc

@@ -0,0 +1,17 @@
+#include "ActionInitialization.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "BeamReactionSteppingAction.hh"
+#include "RunAction.hh"
+
+ActionInitialization::ActionInitialization()
+: G4VUserActionInitialization()
+{}
+
+ActionInitialization::~ActionInitialization() {}
+
+void ActionInitialization::Build() const
+{
+  SetUserAction(new RunAction());
+  SetUserAction(new PrimaryGeneratorAction());
+  SetUserAction(new BeamReactionSteppingAction());
+}

Armory/AnasenG4/src/BeamReactionSteppingAction.cc

@@ -0,0 +1,106 @@
+#include "BeamReactionSteppingAction.hh"
+
+#include "BeamConfig.hh"
+
+#include "ReactionGenerator.hh"
+#include "WireTrackingManager.hh"
+
+#include "G4Step.hh"
+#include "G4Track.hh"
+#include "G4DynamicParticle.hh"
+#include "G4EventManager.hh"
+#include "G4StackManager.hh"
+#include "G4ParticleDefinition.hh"
+#include "G4Proton.hh"
+#include "G4Alpha.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4RandomTools.hh"
+
+#include <cmath>
+
+BeamReactionSteppingAction::BeamReactionSteppingAction()
+: G4UserSteppingAction(),
+  fReaction(new ReactionGenerator())
+{}
+
+BeamReactionSteppingAction::~BeamReactionSteppingAction()
+{
+  delete fReaction;
+}
+
+void BeamReactionSteppingAction::UserSteppingAction(const G4Step* step)
+{
+  WireTrackingManager::Instance().UpdateForStep(step);
+
+  const G4Track* track = step->GetTrack();
+  if (track->GetTrackStatus() != fAlive) {
+    return;
+  }
+
+  const G4ParticleDefinition* particle = track->GetDefinition();
+  if (particle->GetParticleType() != "nucleus") {
+    return;
+  }
+
+  if (particle->GetAtomicNumber() != BeamConfig::kAtomicNumber ||
+      particle->GetAtomicMass() != BeamConfig::kAtomicMass) {
+    return;
+  }
+
+  const auto* prePoint = step->GetPreStepPoint();
+  if (!prePoint || !prePoint->GetPhysicalVolume()) {
+    return;
+  }
+
+  if (prePoint->GetPhysicalVolume()->GetName() != BeamConfig::kTargetVolumeName) {
+    return;
+  }
+
+  const G4double stepLength = step->GetStepLength();
+  if (stepLength <= 0.0) {
+    return;
+  }
+
+  const auto* material = prePoint->GetMaterial();
+  if (!material) {
+    return;
+  }
+
+  const G4double atomDensity = material->GetTotNbOfAtomsPerVolume();
+  const G4double sigma = fReaction->GetEffectiveCrossSection();
+  const G4double probability = 1.0 - std::exp(-atomDensity * sigma * stepLength);
+
+  if (G4UniformRand() > probability) {
+    return;
+  }
+
+  ReactionOutput output = fReaction->SampleEvent(track->GetKineticEnergy(), track->GetMomentumDirection());
+  if (output.kineticEnergy <= 0.0) {
+    return;
+  }
+
+  const G4ThreeVector momentum(output.px, output.py, output.pz);
+  G4ThreeVector direction = momentum;
+  if (direction.mag2() > 0.0) {
+    direction = direction.unit();
+  } else {
+    direction = G4ThreeVector(0.0, 0.0, 1.0);
+  }
+
+  G4ParticleDefinition* product = nullptr;
+  if (output.channel == ReactionChannel::Proton) {
+    product = G4Proton::ProtonDefinition();
+  } else {
+    product = G4Alpha::AlphaDefinition();
+  }
+
+  auto* dynamicParticle = new G4DynamicParticle(product, direction, output.kineticEnergy);
+  auto* secondaryTrack = new G4Track(dynamicParticle, track->GetGlobalTime(), prePoint->GetPosition());
+  secondaryTrack->SetParentID(track->GetTrackID());
+  secondaryTrack->SetTouchableHandle(track->GetTouchableHandle());
+
+  G4EventManager::GetEventManager()->GetStackManager()->PushOneTrack(secondaryTrack, nullptr);
+
+  G4Track* mutableTrack = const_cast<G4Track*>(track);
+  mutableTrack->SetTrackStatus(fStopAndKill);
+}

Armory/AnasenG4/src/DetectorConstruction.cc

@@ -0,0 +1,185 @@
+#include "DetectorConstruction.hh"
+
+#include "DetectorSensitiveDetector.hh"
+
+#include "G4RunManager.hh"
+#include "G4SDManager.hh"
+#include "G4NistManager.hh"
+#include "G4Box.hh"
+#include "G4Tubs.hh"
+#include "G4LogicalVolume.hh"
+#include "G4PVPlacement.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4RotationMatrix.hh"
+#include "G4ThreeVector.hh"
+#include "G4VisAttributes.hh"
+
+DetectorConstruction::DetectorConstruction()
+: G4VUserDetectorConstruction(),
+  fScoringVolume(nullptr),
+  fAnodeLogical(nullptr),
+  fCathodeLogical(nullptr),
+  fSX3Logical(nullptr),
+  fQQQLogical(nullptr)
+{}
+
+DetectorConstruction::~DetectorConstruction()
+{}
+
+G4VPhysicalVolume* DetectorConstruction::Construct()
+{
+  // Get nist material manager
+  G4NistManager* nist = G4NistManager::Instance();
+
+  // Materials
+  G4Material* vacuum = nist->FindOrBuildMaterial("G4_Galactic");
+  G4Material* al = nist->FindOrBuildMaterial("G4_Al");
+
+  // World
+  G4double worldx = 200.*mm;
+  G4double worldy = 200.*mm;
+  G4double worldz = 200.*mm;
+  G4Box* solidWorld = new G4Box("World", worldx, worldy, worldz);
+  G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWorld, vacuum, "World");
+  G4VPhysicalVolume* physWorld = new G4PVPlacement(0, G4ThreeVector(), logicWorld, "World", 0, false, 0, true);
+
+  // Helium target
+
+  G4double pressure = 379.0 * 133.322368 * pascal;
+  G4double temperature = 293.15 * kelvin;
+  G4double density = 8.29e-5 * g/cm3;
+
+  G4Material* HeGas =
+      new G4Material("HeGas",
+                    density,
+                    1,
+                    kStateGas,
+                    temperature,
+                    pressure);
+
+  HeGas->AddElement(nist->FindOrBuildElement("He"), 1);
+  const G4double targetRadius = 37.0*mm;
+  const G4double targetHalfLength = 175.*mm;
+  G4Tubs* solidTarget = new G4Tubs("Target", 0, targetRadius, targetHalfLength, 0, 360*deg);
+  G4LogicalVolume* logicTarget =
+    new G4LogicalVolume(solidTarget, HeGas, "Target");
+  new G4PVPlacement(0, G4ThreeVector(), logicTarget, "Target", logicWorld, false, 0, true);
+  logicTarget->SetVisAttributes(G4VisAttributes::GetInvisible());
+  fScoringVolume = logicTarget;
+
+  // Axes (optional, for visualization)
+  G4Tubs* solidAxis = new G4Tubs("Axis", 0, 0.1*mm, 5.*mm, 0, 360*deg);
+  G4LogicalVolume* logicAxisX = new G4LogicalVolume(solidAxis, al, "AxisX");
+  G4LogicalVolume* logicAxisY = new G4LogicalVolume(solidAxis, al, "AxisY");
+  G4LogicalVolume* logicAxisZ = new G4LogicalVolume(solidAxis, al, "AxisZ");
+
+  G4RotationMatrix* rotX = new G4RotationMatrix();
+  rotX->rotateY(90*deg);
+  rotX->rotateZ(90*deg);
+  new G4PVPlacement(rotX, G4ThreeVector(5*mm, 0, 0), logicAxisX, "AxisX", logicWorld, false, 0);
+
+  G4RotationMatrix* rotY = new G4RotationMatrix();
+  rotY->rotateX(90*deg);
+  new G4PVPlacement(rotY, G4ThreeVector(0, 5*mm, 0), logicAxisY, "AxisY", logicWorld, false, 0);
+
+  new G4PVPlacement(0, G4ThreeVector(0, 0, 5*mm), logicAxisZ, "AxisZ", logicWorld, false, 0);
+
+  // ANASEN geometry
+  const int nWire = 24;
+  const int wireShift = 4;
+  const G4double zLen = 350.*mm;
+  const G4double radiusA = 38.*mm;
+  const G4double radiusC = 43.*mm;
+
+  G4double dAngle = wireShift * 2 * CLHEP::pi / nWire;
+  G4double radiusAnew = radiusA * cos(dAngle / 2.);
+  G4double wireALength = sqrt(zLen*zLen + pow(2 * radiusA * sin(dAngle/2.), 2));
+  G4double wireATheta = atan2(2 * radiusA * sin(dAngle / 2.), zLen);
+
+  G4Tubs* solidPC_A = new G4Tubs("PC_A", 0, .1*mm, wireALength/2., 0, 360*deg);
+  G4LogicalVolume* logicPC_A = new G4LogicalVolume(solidPC_A, al, "PC_A");
+  fAnodeLogical = logicPC_A;
+
+  for(int i = 0; i < nWire; i++){
+    G4double phi = 2 * CLHEP::pi / nWire * i + dAngle / 2.;
+    G4ThreeVector pos(radiusAnew * cos(phi), radiusAnew * sin(phi), 0);
+    // Euler angles: phi (Z), theta (Y), psi (Z)
+    G4double phi_euler = 360./nWire * (i + wireShift/2.) * deg;
+    G4double theta_euler = wireATheta;
+    G4double psi_euler = 0;
+    G4RotationMatrix* rot = new G4RotationMatrix(phi_euler, theta_euler, psi_euler);
+    new G4PVPlacement(rot, pos, logicPC_A, "PC_A", logicWorld, false, i);
+  }
+
+  G4double radiusCnew = radiusC * cos(dAngle / 2.);
+  G4double wireCLength = sqrt(zLen*zLen + pow(2 * radiusC * sin(dAngle/2.), 2));
+  G4double wireCTheta = atan2(2 * radiusC * sin(dAngle / 2.), zLen);
+
+  G4Tubs* solidPC_C = new G4Tubs("PC_C", 0, .1*mm, wireCLength/2., 0, 360*deg);
+  G4LogicalVolume* logicPC_C = new G4LogicalVolume(solidPC_C, al, "PC_C");
+  fCathodeLogical = logicPC_C;
+
+  for(int i = 0; i < nWire; i++){
+    G4double phi = 2 * CLHEP::pi / nWire * i - dAngle/2.;
+    G4ThreeVector pos(radiusCnew * cos(phi), radiusCnew * sin(phi), 0);
+    // Euler angles: phi (Z), theta (Y), psi (Z)
+    G4double phi_euler = 360./nWire * (i - wireShift/2.) * deg;
+    G4double theta_euler = -wireCTheta;
+    G4double psi_euler = 0;
+    G4RotationMatrix* rot = new G4RotationMatrix(phi_euler, theta_euler, psi_euler);
+    new G4PVPlacement(rot, pos, logicPC_C, "PC_C", logicWorld, false, i);
+  }
+
+  const int nSX3 = 12;
+  const G4double sx3Radius = 88.*mm;
+  const G4double sx3Width = 40.*mm;
+  const G4double sx3Length = 75.*mm;
+  const G4double sx3Gap = 5.*mm;
+
+  G4Box* solidSX3 = new G4Box("SX3", 0.1*mm, sx3Width/2., sx3Length/2.);
+  G4LogicalVolume* logicSX3 = new G4LogicalVolume(solidSX3, al, "SX3");
+  fSX3Logical = logicSX3;
+  fScoringVolume = logicSX3;
+
+  for(int i = 0; i < nSX3; i++){
+    G4double phi = 2 * CLHEP::pi / nSX3 * (i + 0.5);
+    G4ThreeVector pos1(sx3Radius * cos(phi), sx3Radius * sin(phi), sx3Length/2. + sx3Gap);
+    // Euler angles: phi (Z), theta (Y), psi (Z)
+    G4double phi_euler = 360./nSX3 * (i + 0.5) * deg;
+    G4RotationMatrix* rot1 = new G4RotationMatrix(phi_euler, 0, 0);
+    new G4PVPlacement(rot1, pos1, logicSX3, "SX3_front", logicWorld, false, 2*i);
+
+    G4ThreeVector pos2(sx3Radius * cos(phi), sx3Radius * sin(phi), -sx3Length/2. - sx3Gap);
+    G4RotationMatrix* rot2 = new G4RotationMatrix(phi_euler, 0, 0);
+    new G4PVPlacement(rot2, pos2, logicSX3, "SX3_back", logicWorld, false, 2*i+1);
+  }
+
+  const G4double qqqR1 = 50.*mm;
+  const G4double qqqR2 = 100.*mm;
+  G4Tubs* solidQQQ = new G4Tubs("QQQ", qqqR1, qqqR2, 0.5*mm, 5*deg, 85*deg);
+  G4LogicalVolume* logicQQQ = new G4LogicalVolume(solidQQQ, al, "QQQ");
+  fQQQLogical = logicQQQ;
+
+  for(int i = 0; i < 4; i++){
+    G4ThreeVector pos(0, 0, 100.*mm);
+    // Euler angles: phi (Z), theta (Y), psi (Z)
+    G4double phi_euler = 360./4 * i * deg;
+    G4RotationMatrix* rot = new G4RotationMatrix(phi_euler, 0, 0);
+    new G4PVPlacement(rot, pos, logicQQQ, "QQQ", logicWorld, false, i);
+  }
+
+  return physWorld;
+}
+
+void DetectorConstruction::ConstructSDandField()
+{
+  auto* detectorSD = new DetectorSensitiveDetector("AnasenSensitiveDetector");
+  G4SDManager::GetSDMpointer()->AddNewDetector(detectorSD);
+
+  if (fSX3Logical != nullptr) {
+    SetSensitiveDetector(fSX3Logical, detectorSD);
+  }
+  if (fQQQLogical != nullptr) {
+    SetSensitiveDetector(fQQQLogical, detectorSD);
+  }
+}

Armory/AnasenG4/src/DetectorSensitiveDetector.cc

@@ -0,0 +1,105 @@
+#include "DetectorSensitiveDetector.hh"
+
+#include "HitOutputManager.hh"
+#include "WireTrackingManager.hh"
+
+#include "G4RunManager.hh"
+#include "G4Step.hh"
+#include "G4Track.hh"
+#include "G4TouchableHistory.hh"
+#include "G4VPhysicalVolume.hh"
+#include "G4StepPoint.hh"
+
+#include <cmath>
+#include <string>
+
+namespace {
+std::string ClassifyDetectorType(const std::string& volumeName)
+{
+  if (volumeName == "PC_A") {
+    return "Anode";
+  }
+  if (volumeName == "PC_C") {
+    return "Cathode";
+  }
+  if (volumeName == "QQQ") {
+    return "QQQ";
+  }
+  if (volumeName.rfind("SX3", 0) == 0) {
+    return "SX3";
+  }
+  return volumeName;
+}
+}
+
+DetectorSensitiveDetector::DetectorSensitiveDetector(const G4String& name)
+: G4VSensitiveDetector(name)
+{}
+
+DetectorSensitiveDetector::~DetectorSensitiveDetector() {}
+
+G4bool DetectorSensitiveDetector::ProcessHits(G4Step* step, G4TouchableHistory*)
+{
+  if (step == nullptr) {
+    return false;
+  }
+
+  G4StepPoint* preStepPoint = step->GetPreStepPoint();
+  if (preStepPoint == nullptr) {
+    return false;
+  }
+
+  G4VPhysicalVolume* volume = preStepPoint->GetPhysicalVolume();
+  if (volume == nullptr) {
+    return false;
+  }
+
+  const G4double kineticEnergy = preStepPoint->GetKineticEnergy();
+  const G4double energyDeposit = step->GetTotalEnergyDeposit();
+  if (kineticEnergy <= 0.0 && energyDeposit <= 0.0) {
+    return false;
+  }
+
+  const G4Event* currentEvent = G4RunManager::GetRunManager()->GetCurrentEvent();
+  if (currentEvent == nullptr) {
+    return false;
+  }
+
+  const std::string particleName = step->GetTrack()->GetParticleDefinition()->GetParticleName();
+  if (!HitOutputManager::Instance().ShouldRecordParticle(particleName)) {
+    return false;
+  }
+
+  const std::string volumeName = volume->GetName();
+  const std::string detectorType = ClassifyDetectorType(volumeName);
+  if (detectorType != "SX3" && detectorType != "QQQ") {
+    return false;
+  }
+
+  WireCrossingInfo wireInfo;
+  WireTrackingManager::Instance().GetInfo(currentEvent->GetEventID(), step->GetTrack()->GetTrackID(), wireInfo);
+  if (wireInfo.anodeId < 0 || wireInfo.cathodeId < 0) {
+    wireInfo = WireTrackingManager::Instance().InferFromTrackGeometry(step->GetTrack(), preStepPoint);
+  }
+
+  const G4ThreeVector trackDirection = step->GetTrack()->GetMomentumDirection();
+  const double sinThetaZ = std::sin(trackDirection.theta());
+  const double wireDeltaESinTheta = wireInfo.deltaE * sinThetaZ;
+
+  HitOutputManager::Instance().RecordHit(currentEvent->GetEventID(),
+                                         particleName,
+                                         kineticEnergy,
+                                         energyDeposit,
+                                         wireDeltaESinTheta,
+                                         detectorType,
+                                         volume->GetCopyNo(),
+                                         wireInfo.anodeId,
+                                         wireInfo.cathodeId,
+                                         wireInfo.anodeEnergy,
+                                         wireInfo.cathodeEnergy,
+                                         wireInfo.deltaE,
+                                         volumeName,
+                                         preStepPoint->GetPosition(),
+                                         step->GetTrack()->GetVertexPosition());
+  return true;
+}

Armory/AnasenG4/src/HitOutputManager.cc

@@ -0,0 +1,279 @@
+#include "HitOutputManager.hh"
+
+#include "TFile.h"
+#include "TH1D.h"
+#include "TH2D.h"
+#include "TTree.h"
+
+#include <cstring>
+#include <iomanip>
+
+namespace {
+const char* kRootOutputName = ANASENG4_DATA_DIR "/hits.root";
+const char* kTextOutputName = ANASENG4_DATA_DIR "/hits.txt";
+}
+
+HitOutputManager& HitOutputManager::Instance()
+{
+  static HitOutputManager instance;
+  return instance;
+}
+
+HitOutputManager::HitOutputManager()
+: fRootFile(nullptr),
+  fTree(nullptr),
+  fEventId(0),
+  fDetectorId(0),
+  fAnodeId(-1),
+  fCathodeId(-1),
+  fKineticEnergy(0.0),
+  fEnergyDeposit(0.0),
+  fWireDeltaESinTheta(0.0),
+  fAnodeEnergy(0.0),
+  fCathodeEnergy(0.0),
+  fWireDeltaE(0.0),
+  fX(0.0),
+  fY(0.0),
+  fZ(0.0),
+  fVertexX(0.0),
+  fVertexY(0.0),
+  fVertexZ(0.0),
+  fKineticEnergyHist(nullptr),
+  fEnergyDepositHist(nullptr),
+  fWireDeltaEHist(nullptr),
+  fWireDeltaESinThetaVsDetEHist(nullptr),
+  fHitZHist(nullptr),
+  fVertexZHist(nullptr),
+  fDetectorIdHist(nullptr),
+  fHitXYHist(nullptr),
+  fVertexXYHist(nullptr),
+  fIncludeElectrons(true)
+{
+  ResetBuffers();
+}
+
+HitOutputManager::~HitOutputManager()
+{
+  Close();
+}
+
+void HitOutputManager::Open()
+{
+  Close();
+
+  fRootFile = TFile::Open(kRootOutputName, "RECREATE");
+  fTree = new TTree("hits", "Sensitive detector hits");
+  fTree->Branch("eventID", &fEventId, "eventID/I");
+  fTree->Branch("particleType", fParticleType, "particleType/C");
+  fTree->Branch("kineticEnergy", &fKineticEnergy, "kineticEnergy/D");
+  fTree->Branch("energyDeposit", &fEnergyDeposit, "energyDeposit/D");
+  fTree->Branch("wireDeltaESinTheta", &fWireDeltaESinTheta, "wireDeltaESinTheta/D");
+  fTree->Branch("detectorType", fDetectorType, "detectorType/C");
+  fTree->Branch("detectorID", &fDetectorId, "detectorID/I");
+  fTree->Branch("anodeID", &fAnodeId, "anodeID/I");
+  fTree->Branch("cathodeID", &fCathodeId, "cathodeID/I");
+  fTree->Branch("anodeEnergy", &fAnodeEnergy, "anodeEnergy/D");
+  fTree->Branch("cathodeEnergy", &fCathodeEnergy, "cathodeEnergy/D");
+  fTree->Branch("wireDeltaE", &fWireDeltaE, "wireDeltaE/D");
+  fTree->Branch("volumeName", fVolumeName, "volumeName/C");
+  fTree->Branch("x", &fX, "x/D");
+  fTree->Branch("y", &fY, "y/D");
+  fTree->Branch("z", &fZ, "z/D");
+  fTree->Branch("vertexX", &fVertexX, "vertexX/D");
+  fTree->Branch("vertexY", &fVertexY, "vertexY/D");
+  fTree->Branch("vertexZ", &fVertexZ, "vertexZ/D");
+
+  fKineticEnergyHist = new TH1D("hKineticEnergy", "Hit kinetic energy;Kinetic energy [MeV];Counts", 200, 0.0, 200.0);
+  fEnergyDepositHist = new TH1D("hEnergyDeposit", "Step energy deposit;Energy deposit [MeV];Counts", 200, 0.0, 50.0);
+  fWireDeltaEHist = new TH1D("hWireDeltaE", "Energy loss between anode and cathode crossings;#DeltaE [MeV];Counts", 200, 0.0, 20.0);
+  fWireDeltaESinThetaVsDetEHist =
+      new TH2D("hWireDeltaESinThetaVsDetE",
+           "PC #DeltaE #times sin(#theta_{z}) vs detector deposited energy;Detector deposited energy [MeV];#DeltaE_{PC} #times sin(#theta_{z}) [MeV]",
+               200,
+               0.0,
+               14.0,
+               200,
+               0.0,
+               20.0);
+  fHitZHist = new TH1D("hHitZ", "Hit z position;z [mm];Counts", 200, -200.0, 200.0);
+  fVertexZHist = new TH1D("hVertexZ", "Track vertex z position;z_{vertex} [mm];Counts", 200, -250.0, 250.0);
+  fDetectorIdHist = new TH1D("hDetectorID", "Detector ID occupancy;Detector ID;Counts", 64, -0.5, 63.5);
+  fHitXYHist = new TH2D("hHitXY", "Hit position;x [mm];y [mm]", 200, -200.0, 200.0, 200, -200.0, 200.0);
+  fVertexXYHist = new TH2D("hVertexXY", "Track vertex position;x_{vertex} [mm];y_{vertex} [mm]", 200, -200.0, 200.0, 200, -200.0, 200.0);
+
+  fTextFile.open(kTextOutputName, std::ios::out | std::ios::trunc);
+  fTextFile << "eventID,particleType,kineticEnergy,energyDeposit,wireDeltaESinTheta,detectorType,detectorID,anodeID,cathodeID,anodeEnergy,cathodeEnergy,wireDeltaE,volumeName,x,y,z,vertexX,vertexY,vertexZ\n";
+}
+
+void HitOutputManager::Close()
+{
+  if (fRootFile != nullptr) {
+    fRootFile->cd();
+    if (fTree != nullptr) {
+      fTree->Write("", TObject::kOverwrite);
+    }
+    if (fKineticEnergyHist != nullptr) {
+      fKineticEnergyHist->Write("", TObject::kOverwrite);
+    }
+    if (fEnergyDepositHist != nullptr) {
+      fEnergyDepositHist->Write("", TObject::kOverwrite);
+    }
+    if (fWireDeltaEHist != nullptr) {
+      fWireDeltaEHist->Write("", TObject::kOverwrite);
+    }
+    if (fWireDeltaESinThetaVsDetEHist != nullptr) {
+      fWireDeltaESinThetaVsDetEHist->Write("", TObject::kOverwrite);
+    }
+    if (fHitZHist != nullptr) {
+      fHitZHist->Write("", TObject::kOverwrite);
+    }
+    if (fVertexZHist != nullptr) {
+      fVertexZHist->Write("", TObject::kOverwrite);
+    }
+    if (fDetectorIdHist != nullptr) {
+      fDetectorIdHist->Write("", TObject::kOverwrite);
+    }
+    if (fHitXYHist != nullptr) {
+      fHitXYHist->Write("", TObject::kOverwrite);
+    }
+    if (fVertexXYHist != nullptr) {
+      fVertexXYHist->Write("", TObject::kOverwrite);
+    }
+    fRootFile->Close();
+    delete fRootFile;
+    fRootFile = nullptr;
+    fTree = nullptr;
+    fKineticEnergyHist = nullptr;
+    fEnergyDepositHist = nullptr;
+    fWireDeltaEHist = nullptr;
+    fWireDeltaESinThetaVsDetEHist = nullptr;
+    fHitZHist = nullptr;
+    fVertexZHist = nullptr;
+    fDetectorIdHist = nullptr;
+    fHitXYHist = nullptr;
+    fVertexXYHist = nullptr;
+  }
+
+  if (fTextFile.is_open()) {
+    fTextFile.close();
+  }
+}
+
+void HitOutputManager::SetIncludeElectrons(bool includeElectrons)
+{
+  fIncludeElectrons = includeElectrons;
+}
+
+bool HitOutputManager::GetIncludeElectrons() const
+{
+  return fIncludeElectrons;
+}
+
+bool HitOutputManager::ShouldRecordParticle(const std::string& particleType) const
+{
+  if (fIncludeElectrons) {
+    return true;
+  }
+
+  return particleType != "e-" && particleType != "e+";
+}
+
+void HitOutputManager::RecordHit(int eventId,
+                                 const std::string& particleType,
+                                 double kineticEnergy,
+                                 double energyDeposit,
+                                 double wireDeltaESinTheta,
+                                 const std::string& detectorType,
+                                 int detectorId,
+                                 int anodeId,
+                                 int cathodeId,
+                                 double anodeEnergy,
+                                 double cathodeEnergy,
+                                 double wireDeltaE,
+                                 const std::string& volumeName,
+                                 const G4ThreeVector& position,
+                                 const G4ThreeVector& vertexPosition)
+{
+  if (fRootFile == nullptr || fTree == nullptr || !fTextFile.is_open()) {
+    return;
+  }
+
+  ResetBuffers();
+
+  fEventId = eventId;
+  fDetectorId = detectorId;
+  fAnodeId = anodeId;
+  fCathodeId = cathodeId;
+  fKineticEnergy = kineticEnergy;
+  fEnergyDeposit = energyDeposit;
+  fWireDeltaESinTheta = wireDeltaESinTheta;
+  fAnodeEnergy = anodeEnergy;
+  fCathodeEnergy = cathodeEnergy;
+  fWireDeltaE = wireDeltaE;
+  fX = position.x();
+  fY = position.y();
+  fZ = position.z();
+  fVertexX = vertexPosition.x();
+  fVertexY = vertexPosition.y();
+  fVertexZ = vertexPosition.z();
+
+  std::strncpy(fParticleType, particleType.c_str(), sizeof(fParticleType) - 1);
+  std::strncpy(fDetectorType, detectorType.c_str(), sizeof(fDetectorType) - 1);
+  std::strncpy(fVolumeName, volumeName.c_str(), sizeof(fVolumeName) - 1);
+
+  fTree->Fill();
+  if (fKineticEnergyHist != nullptr) {
+    fKineticEnergyHist->Fill(fKineticEnergy);
+  }
+  if (fEnergyDepositHist != nullptr) {
+    fEnergyDepositHist->Fill(fEnergyDeposit);
+  }
+  if (fWireDeltaEHist != nullptr && fAnodeId >= 0 && fCathodeId >= 0) {
+    fWireDeltaEHist->Fill(fWireDeltaE);
+  }
+  if (fWireDeltaESinThetaVsDetEHist != nullptr && fAnodeId >= 0 && fCathodeId >= 0) {
+    fWireDeltaESinThetaVsDetEHist->Fill(fEnergyDeposit, 100.0 * fWireDeltaESinTheta); //2D histogram programmed
+  }
+  if (fHitZHist != nullptr) {
+    fHitZHist->Fill(fZ);
+  }
+  if (fVertexZHist != nullptr) {
+    fVertexZHist->Fill(fVertexZ);
+  }
+  if (fDetectorIdHist != nullptr) {
+    fDetectorIdHist->Fill(fDetectorId);
+  }
+  if (fHitXYHist != nullptr) {
+    fHitXYHist->Fill(fX, fY);
+  }
+  if (fVertexXYHist != nullptr) {
+    fVertexXYHist->Fill(fVertexX, fVertexY);
+  }
+
+  fTextFile << fEventId << ','
+            << fParticleType << ','
+            << std::setprecision(12) << fKineticEnergy << ','
+            << fEnergyDeposit << ','
+            << fWireDeltaESinTheta << ','
+            << fDetectorType << ','
+            << fDetectorId << ','
+            << fAnodeId << ','
+            << fCathodeId << ','
+            << fAnodeEnergy << ','
+            << fCathodeEnergy << ','
+            << fWireDeltaE << ','
+            << fVolumeName << ','
+            << fX << ','
+            << fY << ','
+            << fZ << ','
+            << fVertexX << ','
+            << fVertexY << ','
+            << fVertexZ << '\n';
+}
+
+void HitOutputManager::ResetBuffers()
+{
+  fParticleType[0] = '\0';
+  fDetectorType[0] = '\0';
+  fVolumeName[0] = '\0';
+}

Armory/AnasenG4/src/PrimaryGeneratorAction.cc

@@ -0,0 +1,50 @@
+#include "PrimaryGeneratorAction.hh"
+#include "BeamConfig.hh"
+#include "G4ParticleGun.hh"
+#include "G4ParticleTable.hh"
+#include "G4IonTable.hh"
+#include "G4Proton.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4Event.hh"
+#include "G4PhysicalConstants.hh"
+#include "G4RandomTools.hh"
+#include "G4UnitsTable.hh"
+
+#include <cmath>
+
+PrimaryGeneratorAction::PrimaryGeneratorAction()
+: G4VUserPrimaryGeneratorAction(),
+  fParticleGun(nullptr),
+  fBeamRadius(BeamConfig::kRadius),
+  fBeamStartZ(BeamConfig::kStartZ)
+{
+  G4int nParticle = 1;
+  fParticleGun = new G4ParticleGun(nParticle);
+  fParticleGun->SetParticleDefinition(G4Proton::ProtonDefinition());
+  fParticleGun->SetParticleMomentumDirection(G4ThreeVector(0., 0., 1.));
+  fParticleGun->SetParticleEnergy(BeamConfig::kTotalBeamEnergy);
+}
+
+PrimaryGeneratorAction::~PrimaryGeneratorAction()
+{
+  delete fParticleGun;
+}
+
+void PrimaryGeneratorAction::GeneratePrimaries(G4Event* event)
+{
+  auto* ion = G4IonTable::GetIonTable()->GetIon(BeamConfig::kAtomicNumber, BeamConfig::kAtomicMass, 0.0);
+  if (ion) {
+    fParticleGun->SetParticleDefinition(ion);
+  }
+
+  G4double r = fBeamRadius * std::sqrt(G4UniformRand());
+  G4double phi = twopi * G4UniformRand();
+  G4double x = r * std::cos(phi);
+  G4double y = r * std::sin(phi);
+  G4double z = fBeamStartZ;
+
+  fParticleGun->SetParticlePosition(G4ThreeVector(x, y, z));
+  fParticleGun->SetParticleMomentumDirection(G4ThreeVector(0., 0., 1.));
+  fParticleGun->SetParticleEnergy(BeamConfig::kTotalBeamEnergy);
+  fParticleGun->GeneratePrimaryVertex(event);
+}

Armory/AnasenG4/src/ReactionGenerator.cc

@@ -0,0 +1,83 @@
+#include "ReactionGenerator.hh"
+#include "BeamConfig.hh"
+#include "ClassTransfer.h"
+#include "G4SystemOfUnits.hh"
+#include "TRandom.h"
+#include "TVector3.h"
+#include "TLorentzVector.h"
+#include <cmath>
+
+struct ReactionGenerator::Impl {
+  TransferReaction transferP;
+  TransferReaction transferAlpha;
+};
+
+ReactionGenerator::ReactionGenerator()
+: fImpl(nullptr),
+  fEffectiveSigma(5e5 * barn) //originally 5e6
+{
+  // Ensure the isotope mass table is found when running from the AnasenG4 folder.
+  massData = "/home/jamesszalkie/anasen/Armory/mass20.txt";
+  fImpl = new Impl();
+
+  // p-channel: 27Al + 4He -> p + 30Si
+  fImpl->transferP.SetA(BeamConfig::kAtomicMass, BeamConfig::kAtomicNumber, 0);
+  fImpl->transferP.Seta(4, 2);
+  fImpl->transferP.Setb(1, 1);
+  fImpl->transferP.SetB(30, 14, 0);
+
+  // alpha-channel: 27Al + 4He -> alpha + 27Al
+  fImpl->transferAlpha.SetA(BeamConfig::kAtomicMass, BeamConfig::kAtomicNumber, 0);
+  fImpl->transferAlpha.Seta(4, 2);
+  fImpl->transferAlpha.Setb(4, 2);
+  fImpl->transferAlpha.SetB(BeamConfig::kAtomicMass, BeamConfig::kAtomicNumber, 0);
+}
+
+ReactionGenerator::~ReactionGenerator()
+{
+  delete fImpl;
+}
+
+ReactionOutput ReactionGenerator::SampleEvent(double beamKineticEnergy, const G4ThreeVector& beamDirection)
+{
+  // Forward-peaked sampling gives the expected inverse E(theta)-like trend in lab observables.
+  double thetaCM = 0.0;
+  while (true) {
+    const double trial = gRandom->Rndm() * M_PI;
+    const double weight = 1.0 / (1.0 + 20.0 * trial * trial);
+    if (gRandom->Rndm() < weight) {
+      thetaCM = trial;
+      break;
+    }
+  }
+  const double phiCM = gRandom->Rndm() * 2.0 * M_PI;
+
+  const double beamEnergyPerU = beamKineticEnergy / (BeamConfig::kAtomicMass * MeV);
+  const double beamThetaDeg = beamDirection.theta() / deg;
+  const double beamPhiDeg = beamDirection.phi() / deg;
+
+  // Use a mild energy-dependent branching to mix p and alpha events.
+  const double protonFraction = (beamEnergyPerU > 8.0) ? 0.65 : 0.45;
+  const bool isProtonChannel = (gRandom->Rndm() < protonFraction);
+
+  TransferReaction* transfer = isProtonChannel ? &fImpl->transferP : &fImpl->transferAlpha;
+  transfer->SetIncidentEnergyAngle(beamEnergyPerU, beamThetaDeg, beamPhiDeg);
+  transfer->CalReactionConstant();
+
+  TLorentzVector* reactionOutput = transfer->Event(thetaCM, phiCM);
+  TLorentzVector light = reactionOutput[2];
+  delete[] reactionOutput;
+
+  ReactionOutput output;
+  output.channel = isProtonChannel ? ReactionChannel::Proton : ReactionChannel::Alpha;
+  output.kineticEnergy = light.E() - light.M();
+  output.px = light.Px();
+  output.py = light.Py();
+  output.pz = light.Pz();
+  return output;
+}
+
+double ReactionGenerator::GetEffectiveCrossSection() const
+{
+  return fEffectiveSigma;
+}

Armory/AnasenG4/src/RunAction.cc

@@ -0,0 +1,40 @@
+#include "RunAction.hh"
+
+#include "HitOutputManager.hh"
+#include "G4GenericMessenger.hh"
+
+RunAction::RunAction()
+: G4UserRunAction(),
+  fMessenger(nullptr),
+  fIncludeElectrons(false)
+{
+  DefineCommands();
+}
+
+RunAction::~RunAction()
+{
+  delete fMessenger;
+}
+
+void RunAction::DefineCommands()
+{
+  fMessenger = new G4GenericMessenger(this, "/anasen/output/", "ANASEN output controls");
+
+  auto& includeElectronsCmd =
+      fMessenger->DeclareProperty("includeElectrons",
+                                  fIncludeElectrons,
+                                  "Enable or disable recording electron and positron hits.");
+  includeElectronsCmd.SetParameterName("includeElectrons", false);
+  includeElectronsCmd.SetDefaultValue("false");
+}
+
+void RunAction::BeginOfRunAction(const G4Run*)
+{
+  HitOutputManager::Instance().SetIncludeElectrons(fIncludeElectrons);
+  HitOutputManager::Instance().Open();
+}
+
+void RunAction::EndOfRunAction(const G4Run*)
+{
+  HitOutputManager::Instance().Close();
+}

Armory/AnasenG4/src/WireTrackingManager.cc

@@ -0,0 +1,205 @@
+#include "WireTrackingManager.hh"
+
+#include "ClassPW.h"
+
+#include "G4Event.hh"
+#include "G4RunManager.hh"
+#include "G4Step.hh"
+#include "G4StepPoint.hh"
+#include "G4Track.hh"
+#include "G4SystemOfUnits.hh"
+
+#include <algorithm>
+#include <cmath>
+
+namespace {
+constexpr double kAnodeRadius = 37.0 * mm;
+constexpr double kCathodeRadius = 43.0 * mm;
+
+bool CrossesRadius(double preR, double postR, double targetR)
+{
+  return (preR - targetR) * (postR - targetR) <= 0.0 && std::abs(postR - preR) > 1e-12;
+}
+
+TVector3 ToTVector3(const G4ThreeVector& value)
+{
+  return TVector3(value.x(), value.y(), value.z());
+}
+
+bool SolveRadiusIntersection(const G4ThreeVector& origin,
+                             const G4ThreeVector& direction,
+                             double radius,
+                             double& distance)
+{
+  const double a = direction.x() * direction.x() + direction.y() * direction.y();
+  if (a <= 0.0) {
+    return false;
+  }
+
+  const double b = 2.0 * (origin.x() * direction.x() + origin.y() * direction.y());
+  const double c = origin.x() * origin.x() + origin.y() * origin.y() - radius * radius;
+  const double discriminant = b * b - 4.0 * a * c;
+  if (discriminant < 0.0) {
+    return false;
+  }
+
+  const double sqrtDiscriminant = std::sqrt(discriminant);
+  const double t1 = (-b - sqrtDiscriminant) / (2.0 * a);
+  const double t2 = (-b + sqrtDiscriminant) / (2.0 * a);
+
+  distance = -1.0;
+  if (t1 >= 0.0 && t2 >= 0.0) {
+    distance = std::min(t1, t2);
+  } else if (t1 >= 0.0) {
+    distance = t1;
+  } else if (t2 >= 0.0) {
+    distance = t2;
+  }
+
+  return distance >= 0.0;
+}
+}
+
+WireTrackingManager& WireTrackingManager::Instance()
+{
+  static WireTrackingManager instance;
+  return instance;
+}
+
+WireTrackingManager::WireTrackingManager()
+: fCurrentEventId(-1)
+{}
+
+WireTrackingManager::~WireTrackingManager() {}
+
+void WireTrackingManager::EnsureEvent(int eventId)
+{
+  if (eventId != fCurrentEventId) {
+    fCurrentEventId = eventId;
+    fTrackInfo.clear();
+  }
+}
+
+void WireTrackingManager::UpdateForStep(const G4Step* step)
+{
+  if (step == nullptr) {
+    return;
+  }
+
+  const G4Track* track = step->GetTrack();
+  if (track == nullptr) {
+    return;
+  }
+
+  const G4Event* event = G4RunManager::GetRunManager()->GetCurrentEvent();
+  if (event == nullptr) {
+    return;
+  }
+  EnsureEvent(event->GetEventID());
+
+  const G4StepPoint* prePoint = step->GetPreStepPoint();
+  const G4StepPoint* postPoint = step->GetPostStepPoint();
+  if (prePoint == nullptr || postPoint == nullptr) {
+    return;
+  }
+
+  if (prePoint->GetPhysicalVolume() == nullptr || prePoint->GetPhysicalVolume()->GetName() != "Target") {
+    return;
+  }
+
+  if (track->GetDefinition()->GetParticleType() == "nucleus") {
+    return;
+  }
+
+  const G4ThreeVector& prePos = prePoint->GetPosition();
+  const G4ThreeVector& postPos = postPoint->GetPosition();
+  const double preR = prePos.perp();
+  const double postR = postPos.perp();
+
+  if (!CrossesRadius(preR, postR, kAnodeRadius) && !CrossesRadius(preR, postR, kCathodeRadius)) {
+    return;
+  }
+
+  PW pw;
+  pw.ConstructGeo();
+  pw.FindWireID(ToTVector3(track->GetVertexPosition()), ToTVector3(track->GetMomentumDirection()), false);
+
+  auto& info = fTrackInfo[track->GetTrackID()];
+
+  auto interpolateEnergy = [&](double targetR) {
+    const double fraction = (targetR - preR) / (postR - preR);
+    return prePoint->GetKineticEnergy() + fraction * (postPoint->GetKineticEnergy() - prePoint->GetKineticEnergy());
+  };
+
+  if (!info.sawAnode && CrossesRadius(preR, postR, kAnodeRadius)) {
+    info.sawAnode = true;
+    info.anodeId = pw.GetNearestID().first;
+    info.anodeEnergy = interpolateEnergy(kAnodeRadius);
+  }
+
+  if (!info.sawCathode && CrossesRadius(preR, postR, kCathodeRadius)) {
+    info.sawCathode = true;
+    info.cathodeId = pw.GetNearestID().second;
+    info.cathodeEnergy = interpolateEnergy(kCathodeRadius);
+  }
+
+  if (info.sawAnode && info.sawCathode) {
+    info.deltaE = std::abs(info.anodeEnergy - info.cathodeEnergy);
+  }
+}
+
+bool WireTrackingManager::GetInfo(int eventId, int trackId, WireCrossingInfo& info)
+{
+  EnsureEvent(eventId);
+  auto iterator = fTrackInfo.find(trackId);
+  if (iterator == fTrackInfo.end()) {
+    return false;
+  }
+  info = iterator->second;
+  return true;
+}
+
+WireCrossingInfo WireTrackingManager::InferFromTrackGeometry(const G4Track* track, const G4StepPoint* hitPoint)
+{
+  WireCrossingInfo info;
+  if (track == nullptr || hitPoint == nullptr) {
+    return info;
+  }
+
+  const G4ThreeVector origin = track->GetVertexPosition();
+  G4ThreeVector direction = hitPoint->GetPosition() - origin;
+  const double totalPath = direction.mag();
+  if (totalPath <= 0.0) {
+    return info;
+  }
+  direction = direction.unit();
+
+  PW pw;
+  pw.ConstructGeo();
+  pw.FindWireID(ToTVector3(origin), ToTVector3(direction), false);
+  info.anodeId = pw.GetNearestID().first;
+  info.cathodeId = pw.GetNearestID().second;
+
+  const double vertexEnergy = track->GetVertexKineticEnergy();
+  const double hitEnergy = hitPoint->GetKineticEnergy();
+  double anodeDistance = 0.0;
+  double cathodeDistance = 0.0;
+
+  if (SolveRadiusIntersection(origin, direction, 37.0 * mm, anodeDistance)) {
+    const double fraction = std::clamp(anodeDistance / totalPath, 0.0, 1.0);
+    info.anodeEnergy = vertexEnergy + fraction * (hitEnergy - vertexEnergy);
+    info.sawAnode = true;
+  }
+
+  if (SolveRadiusIntersection(origin, direction, 43.0 * mm, cathodeDistance)) {
+    const double fraction = std::clamp(cathodeDistance / totalPath, 0.0, 1.0);
+    info.cathodeEnergy = vertexEnergy + fraction * (hitEnergy - vertexEnergy);
+    info.sawCathode = true;
+  }
+
+  if (info.sawAnode && info.sawCathode) {
+    info.deltaE = std::abs(info.anodeEnergy - info.cathodeEnergy);
+  }
+
+  return info;
+}

Armory/AnasenG4/src/main.cc

@@ -0,0 +1,44 @@
+#include "DetectorConstruction.hh"
+#include "ActionInitialization.hh"
+
+#include "G4RunManagerFactory.hh"
+#include "G4UImanager.hh"
+#include "G4VisExecutive.hh"
+#include "G4UIExecutive.hh"
+#include "G4PhysListFactory.hh"
+
+int main(int argc, char** argv)
+{
+  G4UIExecutive* ui = nullptr;
+  if (argc == 1) {
+    ui = new G4UIExecutive(argc, argv);
+  }
+
+  auto* runManager = G4RunManagerFactory::CreateRunManager(G4RunManagerType::SerialOnly);
+
+  runManager->SetUserInitialization(new DetectorConstruction());
+
+  G4PhysListFactory physListFactory;
+  runManager->SetUserInitialization(physListFactory.GetReferencePhysList("FTFP_BERT"));
+
+  runManager->SetUserInitialization(new ActionInitialization());
+
+  auto* visManager = new G4VisExecutive(argc, argv);
+  visManager->Initialize();
+
+  auto* uiManager = G4UImanager::GetUIpointer();
+
+  if (ui) {
+    uiManager->ApplyCommand("/control/execute init_vis.mac");
+    ui->SessionStart();
+    delete ui;
+  } else {
+    G4String command = "/control/execute ";
+    G4String fileName = argv[1];
+    uiManager->ApplyCommand(command + fileName);
+  }
+
+  delete visManager;
+  delete runManager;
+  return 0;
+}

Armory/AnasenG4/vis.mac

@@ -0,0 +1,31 @@
+
+/vis/open
+/vis/viewer/set/autoRefresh false
+/vis/verbose errors
+
+/vis/drawVolume
+/vis/viewer/set/viewpointVector -1 0 0
+/vis/viewer/set/lightsVector -1 0 0
+/vis/viewer/set/style wireframe
+/vis/viewer/set/auxiliaryEdge true
+/vis/viewer/set/lineSegmentsPerCircle 100
+
+/tracking/storeTrajectory 1
+/vis/scene/add/trajectories smooth
+/vis/modeling/trajectories/create/drawByParticleID
+/vis/modeling/trajectories/drawByParticleID-0/default/setDrawStepPts true
+/vis/modeling/trajectories/drawByParticleID-0/default/setStepPtsSize 2
+/vis/modeling/trajectories/drawByParticleID-0/set proton magenta
+/vis/modeling/trajectories/drawByParticleID-0/set alpha orange
+
+/vis/scene/endOfEventAction accumulate 20
+/vis/geometry/set/visibility World 0 false
+/vis/scene/add/axes 0 0 0 20 mm
+/vis/viewer/set/background 0 0 0
+/vis/viewer/set/style surface
+/vis/viewer/set/hiddenMarker true
+/vis/viewer/set/viewpointThetaPhi 120 150
+
+/vis/viewer/set/autoRefresh true
+/vis/verbose warnings
+/vis/viewer/flush

Armory/AnasenMS.dSYM/Contents/Info.plist

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<key>CFBundleIdentifier</key>
+		<string>com.apple.xcode.dsym.AnasenMS</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundlePackageType</key>
+		<string>dSYM</string>
+		<key>CFBundleSignature</key>
+		<string>????</string>
+		<key>CFBundleShortVersionString</key>
+		<string>1.0</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+	</dict>
+</plist>

Armory/AnasenMS.dSYM/Contents/Resources/Relocations/aarch64/AnasenMS.yml

@@ -0,0 +1,5 @@
+---
+triple:          'arm64-apple-darwin'
+binary-path:     AnasenMS
+relocations:     []
+...

Armory/ClassAnasen.h

@@ -15,6 +15,9 @@
 
 #include "ClassSX3.h"
 #include "ClassPW.h"
+#include "ClassQQQ.h"
+
+//to not include certain wires in the simulation, pass the anode and cathode IDs to the constructor, e.g. for anode wires 5-10, pass anodeID1 = 5, anodeID2 = 10, and for cathode wires 20-25, pass cathodeID1 = 20, cathodeID2 = 25. To include all wires, pass -1 for all IDs.
 
 class ANASEN{
 public:
@@ -41,11 +44,15 @@ public:
 
   PW * GetPW() {return pw;}
   SX3 * GetSX3() {return sx3;}
+  QQQ * GetQQQ() {return qqq;}
+  TGeoManager * GetGeoManager() {return geom;}
+  TGeoVolume * GetWorldBox() {return worldBox;}
 
 private:
 
   PW * pw;
   SX3 * sx3;
+  QQQ * qqq;
 
   double sigmaA, sigmaC; // pw
   double sigmaW, sigmaL; // sx3
@@ -73,7 +80,7 @@ inline ANASEN::ANASEN(){
 
   pw = new PW();
   sx3 = new SX3();
-
+  qqq = new QQQ();
   CalGeometry();
 
   geom = nullptr;
@@ -106,17 +113,21 @@ inline void ANASEN::Construct3DModel(int anodeID1, int anodeID2, int cathodeID1,
   geom = new TGeoManager("Detector", "ANASEN");
 
   //--- define some materials
-  TGeoMaterial *matVacuum = new TGeoMaterial("Vacuum", 0,0,0);
+  //TGeoMaterial *matVacuum = new TGeoMaterial("Vacuum", 0,0,0); //name, A, Z, density 
+  TGeoMaterial *matHe = new TGeoMaterial("He", 4.0026, 2, 0.000861);
   TGeoMaterial *matAl = new TGeoMaterial("Al", 26.98,13,2.7);
+  TGeoMaterial *matSi = new TGeoMaterial("Si", 28.085,14,2.33);
   //--- define some media
-  TGeoMedium *Vacuum = new TGeoMedium("Vacuum",1, matVacuum);
+  //TGeoMedium *Vacuum = new TGeoMedium("Vacuum",1, matVacuum); //name, number of materials, material
+  TGeoMedium *He = new TGeoMedium("He",2, matHe);
   TGeoMedium *Al = new TGeoMedium("Root Material",2, matAl);
+  TGeoMedium *Si = new TGeoMedium("Si",3, matSi);
 
   //--- make the top container volume 
   Double_t worldx = 200.; //mm
   Double_t worldy = 200.; //mm
   Double_t worldz = 200.; //mm
-  worldBox = geom->MakeBox("ROOT", Vacuum, worldx, worldy, worldz);
+  worldBox = geom->MakeBox("ROOT", He, worldx, worldy, worldz); // name, medium, x half-length, y half-length, z half-length
   geom->SetTopVolume(worldBox);
 
   //--- making axis
@@ -181,7 +192,8 @@ inline void ANASEN::Construct3DModel(int anodeID1, int anodeID2, int cathodeID1,
                                                     new TGeoRotation("rot1", wirePhi , wireTheta, 0.)));
   }
 
-  TGeoVolume * sx3Det = geom->MakeBox("box", Al, 0.1, sx3->GetWidth()/2, sx3->GetLength()/2);
+  // Half-thickness is 0.5 mm so full Si thickness is 1.0 mm (0.1 cm).
+  TGeoVolume * sx3Det = geom->MakeBox("box", Si, 0.5, sx3->GetWidth()/2, sx3->GetLength()/2);
   sx3Det->SetLineColor(kGreen+3);
 
   for( int i = 0; i < sx3->GetNumDet(); i++){
@@ -228,6 +240,7 @@ inline  void ANASEN::DrawTrack(TVector3 pos, TVector3 direction, bool drawEstima
 
   pw->FindWireID(pos, direction);
   sx3->FindSX3Pos(pos, direction);
+  qqq->FindQQQPos(pos, direction);
 
   std::pair<short, short> wireID = pw->GetNearestID();
   

Armory/ClassPW.h

@@ -2,17 +2,24 @@
 #define ClassPW_h
 
 #include <cstdio>
+#include <iostream>
 #include <TMath.h>
 #include <TVector3.h>
+#include <TRandom.h>
 
-struct PWHitInfo{
+std::vector<int> skipAnodes = {}; 
+std::vector<int> skipCathodes = {};
+
+struct PWHitInfo
+{
   std::pair<short, short> nearestWire;   // anode, cathode
   std::pair<double, double> nearestDist; // anode, cathode
 
   std::pair<short, short> nextNearestWire;   // anode, cathode
   std::pair<double, double> nextNearestDist; // anode, cathode
 
-  void Clear(){
+  void Clear()
+  {
     nearestWire.first = -1;
     nearestWire.second = -1;
     nearestDist.first = 999999999;
@@ -24,50 +31,74 @@ struct PWHitInfo{
   }
 };
 
-//!########################################################
-class PW{ // proportional wire
+struct Coord
+{
+  float x, y, z;
+  Coord() : x(0), y(0), z(0) {}
+  Coord(const TVector3 &vec)
+  {
+    x = vec.X(); // TVector3's X() returns the x-coordinate
+    y = vec.Y(); // TVector3's Y() returns the y-coordinate
+    z = vec.Z(); // TVector3's Z() returns the z-coordinate
+  }
+};
+
+//! ########################################################
+class PW
+{ // proportional wire
 public:
-  PW(){ ClearHitInfo();};
-  ~PW(){};
+  PW() { ClearHitInfo(); };
+  ~PW() {};
 
-  PWHitInfo GetHitInfo() const {return hitInfo;}
-  std::pair<short, short>   GetNearestID()          const {return hitInfo.nearestWire;}
-  std::pair<double, double> GetNearestDistance()    const {return hitInfo.nearestDist;}
-  std::pair<short, short>   Get2ndNearestID()       const {return hitInfo.nextNearestWire;}
-  std::pair<double, double> Get2ndNearestDistance() const {return hitInfo.nextNearestDist;}
+  PWHitInfo GetHitInfo() const { return hitInfo; }
+  std::pair<short, short> GetNearestID() const { return hitInfo.nearestWire; }
+  std::pair<double, double> GetNearestDistance() const { return hitInfo.nearestDist; }
+  std::pair<short, short> Get2ndNearestID() const { return hitInfo.nextNearestWire; }
+  std::pair<double, double> Get2ndNearestDistance() const { return hitInfo.nextNearestDist; }
 
-  TVector3 GetTrackPos() const {return trackPos;}
-  TVector3 GetTrackVec() const {return trackVec;}
-  double GetTrackTheta() const {return trackVec.Theta();}
-  double GetTrackPhi()   const {return trackVec.Phi();}
+  std::vector<std::pair<TVector3, TVector3>> An; // the anode wire position vector in space
+  std::vector<std::pair<TVector3, TVector3>> Ca; // the cathode wire position vector in space
+
+  TVector3 GetTrackPos() const { return trackPos; }
+  TVector3 GetTrackVec() const { return trackVec; }
+  double GetTrackTheta() const { return trackVec.Theta(); }
+  double GetTrackPhi() const { return trackVec.Phi(); }
   double GetZ0();
 
-  int GetNumWire() const {return nWire;}
-  double GetDeltaAngle() const {return dAngle;}
-  double GetAnodeLength() const {return anodeLength;}
-  double GetCathodeLength() const {return cathodeLength;}
-  TVector3 GetAnodeDn(short id) const {return An[id].first;}
-  TVector3 GetAnodeUp(short id) const {return An[id].second;}
-  TVector3 GetCathodeDn(short id) const {return Ca[id].first;}
-  TVector3 GetCathodeUp(short id) const {return Ca[id].second;}
+  inline std::tuple<std::pair<TVector3, TVector3>, double, double, double>  GetPseudoWire(const std::vector<std::tuple<int,double,double>>& cluster, std::string type);
 
-  TVector3 GetAnodneMid(short id)  const {return (An[id].first + An[id].second) * 0.5; }
-  double   GetAnodeTheta(short id) const {return (An[id].first - An[id].second).Theta();}
-  double   GetAnodePhi(short id)   const {return (An[id].first - An[id].second).Phi();}
+  inline std::tuple<TVector3,double,double,double,double,double,double,double> 
+  FindCrossoverProperties(const std::vector<std::tuple<int,double,double>>& a_cluster, const std::vector<std::tuple<int,double,double>>& c_cluster);
 
-  TVector3 GetCathodneMid(short id)  const {return (Ca[id].first + Ca[id].second) * 0.5; }
-  double   GetCathodeTheta(short id) const {return (Ca[id].first - Ca[id].second).Theta();}
-  double   GetCathodePhi(short id)   const {return (Ca[id].first - Ca[id].second).Phi();}
+  inline std::vector<std::vector<std::tuple<int,double,double>>>
+  Make_Clusters(std::unordered_map<int,std::tuple<int,double,double>> wireEvents);
+	
+  int GetNumWire() const { return nWire; }
+  double GetDeltaAngle() const { return dAngle; }
+  double GetAnodeLength() const { return anodeLength; }
+  double GetCathodeLength() const { return cathodeLength; }
+  TVector3 GetAnodeDn(short id) const { return An[id].first; }
+  TVector3 GetAnodeUp(short id) const { return An[id].second; }
+  TVector3 GetCathodeDn(short id) const { return Ca[id].first; }
+  TVector3 GetCathodeUp(short id) const { return Ca[id].second; }
+
+  TVector3 GetAnodneMid(short id) const { return (An[id].first + An[id].second) * 0.5; }
+  double GetAnodeTheta(short id) const { return (An[id].first - An[id].second).Theta(); }
+  double GetAnodePhi(short id) const { return (An[id].first - An[id].second).Phi(); }
+
+  TVector3 GetCathodneMid(short id) const { return (Ca[id].first + Ca[id].second) * 0.5; }
+  double GetCathodeTheta(short id) const { return (Ca[id].first - Ca[id].second).Theta(); }
+  double GetCathodePhi(short id) const { return (Ca[id].first - Ca[id].second).Phi(); }
 
   void ClearHitInfo();
   void ConstructGeo();
   void FindWireID(TVector3 pos, TVector3 direction, bool verbose = false);
   void CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose = false);
-  void CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA = 0, double sigmaC = 0, bool verbose = false);
+  //void CalTrack2(TVector3 sx3Pos, TVector3 anodeInt, bool verbose = false);
+  void CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose);
 
-  double CircularMean(std::vector<std::pair<int, double>> wireList);
-
-  void Print(){
+  void Print()
+  {
     printf("     The nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nearestWire.first,
            hitInfo.nearestDist.first,
            hitInfo.nearestWire.second,
@@ -80,7 +111,6 @@ public:
   }
 
 private:
-
   PWHitInfo hitInfo;
 
   TVector3 trackPos;
@@ -88,7 +118,8 @@ private:
 
   const int nWire = 24;
   const int wireShift = 3;
-  const float zLen = 380; //mm
+  //const float zLen = 380; // mm
+  const float zLen = 348.6; // mm
   const float radiusA = 37;
   const float radiusC = 43;
 
@@ -96,23 +127,25 @@ private:
   double anodeLength;
   double cathodeLength;
 
-  std::vector<std::pair<TVector3,TVector3>> An; // the anode wire position vector in space 
-  std::vector<std::pair<TVector3,TVector3>> Ca; // the cathode wire position vector in space 
+  // std::vector<std::pair<TVector3, TVector3>> An; // the anode wire position vector in space
+  // std::vector<std::pair<TVector3, TVector3>> Ca; // the cathode wire position vector in space
 
-  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2){
+  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2)
+  {
     TVector3 na = a1 - a2;
     TVector3 nb = b1 - b2;
     TVector3 nd = (na.Cross(nb)).Unit();
-    return TMath::Abs(nd.Dot(a1-b2));
+    return TMath::Abs(nd.Dot(a1 - b2));
   }
-
 };
 
-inline void PW::ClearHitInfo(){
+inline void PW::ClearHitInfo()
+{
   hitInfo.Clear();
 }
 
-inline void PW::ConstructGeo(){
+inline void PW::ConstructGeo()
+{
 
   An.clear();
   Ca.clear();
@@ -120,108 +153,296 @@ inline void PW::ConstructGeo(){
   std::pair<TVector3, TVector3> p1; // anode
   std::pair<TVector3, TVector3> q1; // cathode
 
-  //anode and cathode start at pos-Y axis and count in right-Hand
-  //anode wire shift is right-hand.
-  //cathode wire shift is left-hand.
+  // anode and cathode start at pos-Y axis and count in right-Hand
+  // anode wire shift is right-hand.
+  // cathode wire shift is left-hand.
 
-  for(int i = 0; i < nWire; i++ ){
+  for (int i = 0; i < nWire; i++)
+  {
     // Anode rotate right-hand
-    p1.first.SetXYZ( radiusA * TMath::Cos( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    radiusA * TMath::Sin( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    zLen/2);
-    p1.second.SetXYZ( radiusA * TMath::Cos( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
-                      radiusA * TMath::Sin( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
-                    -zLen/2);
+    p1.first.SetXYZ(radiusA * TMath::Cos(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    radiusA * TMath::Sin(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    zLen / 2);
+    p1.second.SetXYZ(radiusA * TMath::Cos(TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+                     radiusA * TMath::Sin(TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+                     -zLen / 2);
     An.push_back(p1);
 
-    // Cathod rotate left-hand
-    q1.first.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    zLen/2);
-    q1.second.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
-                      radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
-                      -zLen/2);
+    // Cathod rotate left-hand with the 3 wire offset accounted for (+1 from the calculated offset from the PC coincidence spectrum)
+    q1.first.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i + wireShift + 1) + TMath::PiOver2()),
+                    radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i + wireShift + 1) + TMath::PiOver2()),
+                    zLen / 2);
+    q1.second.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i + 1) + TMath::PiOver2()),
+                     radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i + 1) + TMath::PiOver2()),
+                     -zLen / 2);
     Ca.push_back(q1);
   }
+  // correcting for the fact that the order of the cathode wires is reversed
+  std::reverse(Ca.begin(), Ca.end());
+  // adjusting for the 3 wire offset, the rbegin and rend are used as the rotation of the wires is done in the opposite direction i.e. 1,2,3 -> 3,1,2
+  // NOT NECESSARY ANY MORE, HAS BEEN IMCORPORATED INTO THE WIREOFFSET IN THE BEGINNING
+  // std::rotate(Ca.rbegin(), Ca.rbegin() + 4, Ca.rend());
 
   dAngle = wireShift * TMath::TwoPi() / nWire;
-  anodeLength = TMath::Sqrt( zLen*zLen + TMath::Power(2* radiusA * TMath::Sin(dAngle/2),2) );
-  cathodeLength = TMath::Sqrt( zLen*zLen + TMath::Power(2* radiusC * TMath::Sin(dAngle/2),2) );
+  anodeLength = TMath::Sqrt(zLen * zLen + TMath::Power(2 * radiusA * TMath::Sin(dAngle / 2), 2));
+  cathodeLength = TMath::Sqrt(zLen * zLen + TMath::Power(2 * radiusC * TMath::Sin(dAngle / 2), 2)); //chord length subtending an angle alpha is 2rsin(alpha/2)
 }
 
-inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
+inline std::vector<std::vector<std::tuple<int,double,double>>>
+PW::Make_Clusters(std::unordered_map<int,std::tuple<int,double,double>> wireEvents) {
+   std::vector<std::vector<std::tuple<int,double,double>>> wireClusters;
+   std::vector<std::tuple<int,double,double>> wireCluster;
+	//TODO: Write a macro once, call it twice
+    int wirecount=0;
+	while(wirecount < 24) {
+		if(wireEvents.find(wirecount)==wireEvents.end()) {
+				wirecount++;
+				continue;
+		}
+		wireCluster.clear();
+		int ctr2=wirecount;
+		do {
+			wireCluster.emplace_back(wireEvents[ctr2]);
+			ctr2+=1;
+			if(ctr2==24 || ctr2-wirecount == 7) break; //loose logic, needs to be looked at.
+		} while(wireEvents.find(ctr2)!=wireEvents.end());
+		wireClusters.push_back(std::move(wireCluster));
+		wirecount = ctr2; //we already dealt with wires until the last value of ctr2
+	}
 
+	if(wireClusters.size() > 1) { //Deal with wraparound if required
+		auto first_cluster = wireClusters.front(); //front and back provide references to the elements themselves. less copy, can modify etc
+		auto last_cluster = wireClusters.back();
+		if(std::get<0>(last_cluster.back())==23 && std::get<0>(first_cluster.front())==0) {
+			last_cluster.insert(last_cluster.end(),first_cluster.begin(),first_cluster.end());
+		}
+		wireClusters.erase(wireClusters.begin()); //canonically, erase() needs an iterator, hence begin() not front()
+		//TODO: Can also deal with 'gaps' of missing wires similarly. end of one segment and beginning of another segment will be separated by missing wire --> combine the two
+		//TODO: Also needs some development regarding the time-correlation. Don't put wires in the same cluster if they aren't time coincident
+	}
+	return wireClusters;
+
+  /*if(aClusters.size()>1 || cClusters.size() > 1) {
+  	std::cout << " ============== " << std::endl;
+  }
+  if(aClusters.size()>1 && cClusters.size() >=1) {
+  	std::cout << aClusters.size() << " new anode clusters ----> " << std::endl;
+  	int cc=1;
+  	for(auto ac : aClusters) {
+  		std::cout << "  Cluster " << cc << std::endl;
+	  	double first_ts = std::get<2>(ac.at(0));
+  		for(auto item : ac) {
+	  		std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+  		}
+  		std::cout << "  ------" << std::endl;
+  		cc++;
+  	}
+  } 	
+
+  if(cClusters.size()>=1 ) {
+  	std::cout << cClusters.size() << " new cathode clusters ----> " << std::endl;
+  	int cc=1;
+  	for(auto ac : cClusters) {
+  		std::cout << "  Cluster " << cc << std::endl;
+	  	double first_ts = std::get<2>(ac.at(0));
+  		for(auto item : ac) {
+	  		std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+  		}
+  		std::cout << "  ------" << std::endl;
+  		cc++;
+  	}
+  } 	*/
+}
+
+inline std::tuple<std::pair<TVector3, TVector3>, double, double, double>
+PW::GetPseudoWire(const std::vector<std::tuple<int,double,double>>& cluster, std::string type) {
+	std::pair<TVector3,TVector3> avgvec = std::pair(TVector3(0,0,0),TVector3(0,0,0));
+	double sumEnergy = 0;
+	double maxEnergy = 0;
+	double tsMaxEnergy = 0;
+	if(type=="ANODE") {
+		//if(cluster.size()>1) std::cout << " -------anodes" << std::endl;
+		for( auto wire : cluster) {
+			avgvec.first += std::get<1>(wire)*TVector3(An.at(std::get<0>(wire)).first.X(), An.at(std::get<0>(wire)).first.Y(), 0) ;
+			avgvec.second += std::get<1>(wire)*TVector3(An.at(std::get<0>(wire)).second.X(), An.at(std::get<0>(wire)).second.Y(), 0);
+			sumEnergy += std::get<1>(wire);
+			if(std::get<1>(wire) > maxEnergy) {
+				maxEnergy = std::get<1>(wire);
+				tsMaxEnergy = std::get<2>(wire);
+			}
+			/*if(cluster.size()>1) {
+				std::cout << "\t\t ch:" << std::get<0>(wire) << " " << std::get<1>(wire) << " " << std::get<2>(wire) << std::endl;
+				std::cout << "\t\t w1(r,phi,z):" << An.at(std::get<0>(wire)).first.Perp() << " " << An.at(std::get<0>(wire)).first.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).first.Z() << std::endl;
+				std::cout << "\t\t w2(r,phi,z):" << An.at(std::get<0>(wire)).second.Perp() << " " << An.at(std::get<0>(wire)).second.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).second.Z() << std::endl;			
+			}*/
+		}
+		avgvec.first = avgvec.first*(1.0/sumEnergy);
+		avgvec.second = avgvec.second*(1.0/sumEnergy);
+		double phi1 = avgvec.first.Phi();
+		double phi2 = avgvec.second.Phi();
+		avgvec.first.SetXYZ(radiusA*TMath::Cos(phi1), radiusA*TMath::Sin(phi1), zLen/2);
+		avgvec.second.SetXYZ(radiusA*TMath::Cos(phi2), radiusA*TMath::Sin(phi2), -zLen/2);
+		/*if(cluster.size()>1) {
+			std::cout << "\t\t avg1(r,phi,z):" << avgvec.first.Perp() << " " << avgvec.first.Phi()*180/M_PI << " " << avgvec.first.Z() << std::endl;			
+			std::cout << "\t\t avg2(r,phi,z):" << avgvec.second.Perp() << " " << avgvec.second.Phi()*180/M_PI << " " << avgvec.second.Z() << std::endl;			
+		}*/	
+	} else if(type =="CATHODE") {
+		for( auto wire : cluster) {
+			avgvec.first += std::get<1>(wire)*TVector3(Ca.at(std::get<0>(wire)).first.X(), Ca.at(std::get<0>(wire)).first.Y(), 0) ;
+			avgvec.second += std::get<1>(wire)*TVector3(Ca.at(std::get<0>(wire)).second.X(), Ca.at(std::get<0>(wire)).second.Y(), 0);
+			sumEnergy += std::get<1>(wire);
+			if(std::get<1>(wire) > maxEnergy) {
+				maxEnergy = std::get<1>(wire);
+				tsMaxEnergy = std::get<2>(wire);
+			}
+		}
+		avgvec.first = avgvec.first*(1.0/sumEnergy);
+		avgvec.second = avgvec.second*(1.0/sumEnergy);
+		double phi1 = avgvec.first.Phi();
+		double phi2 = avgvec.second.Phi();
+		avgvec.first.SetXYZ(radiusC*TMath::Cos(phi1), radiusC*TMath::Sin(phi1), zLen/2);
+		avgvec.second.SetXYZ(radiusC*TMath::Cos(phi2), radiusC*TMath::Sin(phi2), -zLen/2);	
+	}
+	return std::tuple(avgvec, sumEnergy, maxEnergy, tsMaxEnergy); 
+}
+
+inline std::tuple<TVector3,double,double,double,double,double,double,double> PW::FindCrossoverProperties(const std::vector<std::tuple<int,double,double>>& a_cluster,
+																				 const std::vector<std::tuple<int,double,double>>& c_cluster) {
+	//std::pair<TVector3, TVector3> apwire = GetPseudoWire(a_cluster,"ANODE",anodeSumE);
+	//std::pair<TVector3, TVector3> cpwire = GetPseudoWire(c_cluster,"CATHODE",cathodeSumE);
+	auto [apwire, apSumE, apMaxE, apTSMaxE] = GetPseudoWire(a_cluster,"ANODE");
+	auto [cpwire, cpSumE, cpMaxE, cpTSMaxE] = GetPseudoWire(c_cluster,"CATHODE");
+
+	TVector3 crossover;
+	crossover.Clear();
+  	TVector3 a, c, diff;
+  	double a2, ac, c2, adiff, cdiff, denom, alpha=0;
+
+	if(apSumE && cpSumE) {
+    	a = apwire.first - apwire.second;
+		c = cpwire.first - cpwire.second;
+      	diff = apwire.first - cpwire.first;
+      	a2 = a.Dot(a);
+      	c2 = c.Dot(c);
+      	ac = a.Dot(c);
+      	adiff = a.Dot(diff);
+      	cdiff = c.Dot(diff);
+      	denom = a2 * c2 - ac * ac;
+      	alpha = (ac * cdiff - c2 * adiff) / denom;
+		crossover = apwire.first + alpha*a;		
+		if(crossover.z() < -190 || crossover.Z() > 190 ) {
+			alpha = 9999999;
+			apSumE=-1; cpSumE=-1;
+			apMaxE=-1; cpMaxE=-1;
+			apTSMaxE=-1; cpTSMaxE=-1;
+		}
+	}
+	//std::cout << apSumE << " " << cpSumE << " " << " " <<  crossover.Perp() << std::endl;
+	return std::tuple(crossover,alpha,apSumE,cpSumE,apMaxE,cpMaxE,apTSMaxE,cpTSMaxE);
+}
+
+inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose)
+{
+//to skip certain wires, add their IDs to the skipAnodes and skipCathodes vectors above, then in this function, add a check to set the distance to a large number if the wire ID is in the skip list, e.g. if(std::find(skipAnodes.begin(), skipAnodes.end(), i) != skipAnodes.end()) { disA = 99999999; } to skip anode wire i, and if(std::find(skipCathodes.begin(), skipCathodes.end(), i) != skipCathodes.end()) { disC = 99999999; } to skip cathode wire i.
+//do this on the line before the line "if (phiS < phi && phi < phiL)" in the anode and cathode loops below, respectively, so that the wires will be marked as invalid and not used in track reconstruction
   hitInfo.Clear();
   double phi = direction.Phi();
 
-  for( int i = 0; i < nWire; i++){
+  for (int i = 0; i < nWire; i++)
+  {
 
     double disA = 99999999;
     double phiS = An[i].first.Phi() - TMath::PiOver4();
     double phiL = An[i].second.Phi() + TMath::PiOver4();
     // printf("A%2d: %f %f | %f\n", i, phiS * TMath::RadToDeg(), phiL * TMath::RadToDeg(), phi * TMath::RadToDeg());
-    if( phi > 0 && phiS > phiL )  phiL = phiL + TMath::TwoPi();
-    if( phi < 0 && phiS > phiL )  phiS = phiS - TMath::TwoPi();
-
-    if( phiS < phi && phi < phiL) {
-      disA = Distance( pos, pos + direction, An[i].first, An[i].second);
-      if( disA < hitInfo.nearestDist.first ){
+    if (phi > 0 && phiS > phiL)
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();
+    if(std::find(skipAnodes.begin(), skipAnodes.end(), i) != skipAnodes.end()) { // check if the current anode wire ID is in the skipAnodes vector
+      disA = 99999999;
+    }
+    if (phiS < phi && phi < phiL) // check if the track direction is within the angular range of the wire
+    {
+      disA = Distance(pos, pos + direction, An[i].first, An[i].second);
+      if (disA < hitInfo.nearestDist.first)
+      {
         hitInfo.nearestDist.first = disA;
         hitInfo.nearestWire.first = i;
       }
     }
 
     double disC = 99999999;
-    phiS = Ca[i].second.Phi()- TMath::PiOver4();
+    phiS = Ca[i].second.Phi() - TMath::PiOver4();
     phiL = Ca[i].first.Phi() + TMath::PiOver4();
     // printf("C%2d: %f %f\n", i, phiS * TMath::RadToDeg(), phiL * TMath::RadToDeg());
-    if( phi > 0 && phiS > phiL ) phiL = phiL + TMath::TwoPi();
-    if( phi < 0 && phiS > phiL ) phiS = phiS - TMath::TwoPi();
+    if(std::find(skipCathodes.begin(), skipCathodes.end(), i) != skipCathodes.end()) { // check if the current cathode wire ID is in the skipCathodes vector
+      disC = 99999999;
+    }
+    if (phi > 0 && phiS > phiL)
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();
 
-    if(phiS < phi && phi < phiL) {
-      disC = Distance( pos, pos + direction, Ca[i].first, Ca[i].second);
-      if( disC < hitInfo.nearestDist.second ){
+    if (phiS < phi && phi < phiL)
+    {
+      disC = Distance(pos, pos + direction, Ca[i].first, Ca[i].second);
+      if (disC < hitInfo.nearestDist.second)
+      {
         hitInfo.nearestDist.second = disC;
         hitInfo.nearestWire.second = i;
       }
     }
 
-    if(verbose) printf(" %2d | %8.2f, %8.2f\n", i, disA, disC);
+    if (verbose)
+      printf(" %2d | %8.2f, %8.2f\n", i, disA, disC);
   }
 
   //==== find the 2nd nearest wire
   short anode1 = hitInfo.nearestWire.first;
-  short aaa1 = anode1 - 1; if( aaa1 < 0 ) aaa1 += nWire;
+  short aaa1 = anode1 - 1;
+  if (aaa1 < 0)
+    aaa1 += nWire;
   short aaa2 = (anode1 + 1) % nWire;
 
-  double haha1 = Distance( pos, pos + direction, An[aaa1].first, An[aaa1].second);
-  double haha2 = Distance( pos, pos + direction, An[aaa2].first, An[aaa2].second);
-  if( haha1 < haha2){
+  double haha1 = Distance(pos, pos + direction, An[aaa1].first, An[aaa1].second);
+  double haha2 = Distance(pos, pos + direction, An[aaa2].first, An[aaa2].second);
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.first = aaa1;
     hitInfo.nextNearestDist.first = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.first = aaa2;
     hitInfo.nextNearestDist.first = haha2;
   }
 
   short cathode1 = hitInfo.nearestWire.second;
-  short ccc1 = cathode1 - 1; if( ccc1 < 0 ) ccc1 += nWire;
+  short ccc1 = cathode1 - 1;
+  if (ccc1 < 0)
+    ccc1 += nWire;
   short ccc2 = (cathode1 + 1) % nWire;
 
-  haha1 = Distance( pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
-  haha2 = Distance( pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
-  if( haha1 < haha2){
+  haha1 = Distance(pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
+  haha2 = Distance(pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.second = ccc1;
     hitInfo.nextNearestDist.second = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.second = ccc2;
     hitInfo.nextNearestDist.second = haha2;
   }
 
-  if( verbose ) Print();
+  if (verbose)
+    Print();
 }
 
-inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose){
+inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose)
+{
 
   trackPos = sx3Pos;
 
@@ -231,11 +452,13 @@ inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbo
   // if the handiness of anode and cathode revered, it should be n2 cross n1
   trackVec = (n2.Cross(n1)).Unit();
 
-  if( verbose ) printf("Theta, Phi = %f, %f \n", trackVec.Theta() *TMath::RadToDeg(), trackVec.Phi()*TMath::RadToDeg()); 
-
+  if (verbose)
+    printf("Theta, Phi = %f, %f \n", trackVec.Theta() * TMath::RadToDeg(), trackVec.Phi() * TMath::RadToDeg());
 }
 
-inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose){
+
+inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose)
+{
 
   trackPos = sx3Pos;
 
@@ -267,36 +490,31 @@ inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, dou
   // if the handiness of anode and cathode revered, it should be n2 cross n1
   trackVec = (n2.Cross(n1)).Unit();
 
-  if( verbose ) printf("Theta, Phi = %f, %f \n", trackVec.Theta() *TMath::RadToDeg(), trackVec.Phi()*TMath::RadToDeg()); 
-
+  if (verbose)
+    printf("Theta, Phi = %f, %f \n", trackVec.Theta() * TMath::RadToDeg(), trackVec.Phi() * TMath::RadToDeg());
 }
 
-inline double PW::GetZ0(){
+/*inline TVector3 PW::CalTrack3(TVector3 siPos, TVector3 anodeInt, bool verbose)
+{
 
-  double x = trackPos.X();
-  double y = trackPos.Y();
-  double rho = TMath::Sqrt(x*x + y*y);
-  double theta = trackVec.Theta();
+  TVector3 v = anodeInt-siPos;
+  double t_minimum = -1.0*(siPos.X()*v.X()+siPos.Y()*v.Y())/(v.X()*v.X()+v.Y()*v.Y());
+  TVector3 vector_closest_to_z = siPos + t_minimum*v;
 
-  return trackPos.Z() - rho / TMath::Tan(theta);
+  return vector_closest_to_z;
+  if (verbose)
+    printf("X slope = %f and Y slope = %f \n", mx, my);
+}*/
 
-}
+inline double PW::GetZ0()
+{
 
-inline double PW::CircularMean(std::vector<std::pair<int, double>> wireList){
-
-  //use unit vector, wireID start from Zero
-  double xCom = 0, yCom = 0;
-  for( size_t i = 0; i < wireList.size() ; i++){
-    xCom += TMath::Cos(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
-    yCom += TMath::Sin(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
-  }
-
-  //calculate the angle of the summed unit vectors
-  double angle = TMath::ATan2(yCom, xCom);
-  if( angle < 0 ) angle += TMath::TwoPi(); // convert the angle from 0 to 2 pi
-
-  return angle/ TMath::TwoPi() * nWire;
+  [[maybe_unused]]double x = trackPos.X();
+  [[maybe_unused]]double y = trackPos.Y();
+  [[maybe_unused]]double rho = TMath::Sqrt(x * x + y * y);
+  [[maybe_unused]]double theta = trackVec.Theta();
 
+  return trackVec.Z();
 }
 
 #endif

Armory/ClassQQQ.h

@@ -0,0 +1,280 @@
+#ifndef ClassQQQ_h
+#define ClassQQQ_h
+
+#include <cstdio>
+#include <TMath.h>
+#include <TVector3.h>
+#include <TRandom.h>
+#include "TGeoManager.h"
+#include "TGeoVolume.h"
+#include "TGeoBBox.h"
+
+class QQQ{
+public:
+  QQQ(){Clear();};
+  ~QQQ(){}
+  
+  short GetID() const {return id;}
+  short GetChUp() const {return chUp;}
+  short GetChDn() const {return chDn;}
+  short GetChBk() const {return chBk;}
+
+  TVector3 GetHitPos() const {return hitPos;}
+  TVector3 GetHitPosWithSigma(double sigmaY_mm, double sigmaZ_mm);
+
+  double GetZFrac() const {return zFrac;} // range from -0.5 to 0.5
+
+  void Clear();
+  void ConstructGeo();
+  void FindQQQPos(TVector3 pos, TVector3 direction, bool verbose = false);
+  void CalQQQPos(unsigned short ID, unsigned short chUp, unsigned short chDown, unsigned short chBack, float eUp, float eDown);
+
+  double GetNumDet() const {return numDet;}
+
+  void Print(){ 
+    if( id == -1 ){
+      printf("Did not hit any QQQ.\n"); 
+    }else{
+      printf("ID: %d, U,D,B: %d %d %d| zFrac : %.2f\n", id, chUp, chDn, chBk, zFrac); 
+      printf("Hit Pos: %.2f, %.2f, %.2f\n", hitPos.X(), hitPos.Y(), hitPos.Z()); 
+    }
+  }
+
+  // void CalZFrac(){
+  //   zFrac = (eUp - eDn)/(eUp + eDn); 
+  // }
+
+private:
+
+  const int numDet = 4;
+  const float qqqR1 = 50;
+  const float qqqR2 = 100;
+  const float qqqZPos = 23 + 75 + 30;
+
+  short id; // -1 when no hit
+  short chUp;
+  short chDn;
+  short chBk;
+
+  double zFrac; // from +1 (downstream) to -1 (upstream)
+
+  double eUp;
+  double eDn;
+  double eBk;
+
+  TVector3 hitPos;
+
+  TGeoManager *geom;
+  TGeoVolume *worldBox;
+  TGeoMedium *Al;
+
+  // helper function to calculate intersection between line segments, return pair of (fraction along line1, fraction along line2) where the intersection occurs. If no intersection, return (0, -1).
+  std::pair<double, double> Intersect(TVector3 p1, TVector3 p2, TVector3 q1, TVector3 q2, bool verbose){ 
+
+    //see https://nukephysik101.wordpress.com/2023/12/30/intersect-between-2-line-segments/
+    //zero all z-component
+    TVector3 a0 = p1; a0.SetZ(0);
+    TVector3 a1 = p2; a1.SetZ(0);
+
+    TVector3 b0 = q1; b0.SetZ(0);
+    TVector3 b1 = q2; b1.SetZ(0);
+
+    double h = 0, k = 0; // placeholder values, implementation of intersection logic
+    if( verbose ) printf(" ----h, k : %f, %f\n", h, k);
+
+    return std::pair<double,double>(h,k);
+  }
+
+};
+
+inline void QQQ::Clear(){
+  id = -1;
+  chUp = -1;
+  chDn = -1;
+  chBk = -1;
+  zFrac = TMath::QuietNaN();
+
+  eUp = TMath::QuietNaN();
+  eDn = TMath::QuietNaN();
+  eBk = TMath::QuietNaN();
+}
+
+inline void QQQ::ConstructGeo(){
+  TGeoVolume *qqq = geom->MakeTubs("qqq", Al, qqqR1, qqqR2, 0.5, 5, 85); // thickness 0.5 mm, phi from 5 to 90 deg in each quadrant
+  qqq->SetLineColor(7);
+  for( int i = 0; i < 4; i++){
+    worldBox->AddNode(qqq, i+1, new TGeoCombiTrans( 0,
+                                                    0, 
+                                                    qqqZPos, 
+                                                    new TGeoRotation("rot1", 360/4 * (i), 0., 0.))); //arguments are (name, material, inner radius, outer radius, half length in z, start phi, delta phi
+  }
+}
+
+
+inline void QQQ::FindQQQPos(TVector3 pos,
+                            TVector3 direction,
+                            bool verbose){
+
+  id   = -1;
+  chUp = -1;
+  chDn = -1;
+  chBk = -1;
+
+  if( TMath::Abs(direction.Z()) < 1e-10 ) return;
+
+  double t = (qqqZPos - pos.Z()) / direction.Z();
+
+  if( t <= 0 ) return;
+
+  hitPos = pos + t * direction;
+
+  //--------------------------------------------
+  // Cylindrical coordinates
+  //--------------------------------------------
+
+  double x = hitPos.X();
+  double y = hitPos.Y();
+
+  double r = TMath::Sqrt(x*x + y*y);
+
+  if( r < qqqR1 || r > qqqR2 ) return;
+
+  double phi = hitPos.Phi() * TMath::RadToDeg();
+
+  if( phi < 0 ) phi += 360.0;
+
+  //--------------------------------------------
+  // Determine detector ID
+  //--------------------------------------------
+
+  id = -1;
+
+  for(int det = 0; det < 4; det++){
+
+    double phiMin = det*90.0 + 5.0;
+    double phiMax = phiMin + 85.0;
+
+    if( phi >= phiMin && phi <= phiMax ){
+      id = det;
+      break;
+    }
+  }
+
+  if( id < 0 ) return;
+
+  const double ringWidth =
+      (qqqR2 - qqqR1)/32.0;
+
+  int ring =
+      (int)((r - qqqR1)/ringWidth);
+
+  if( ring < 0 ) ring = 0;
+  if( ring > 31 ) ring = 31;
+
+  //--------------------------------------------
+  // Sector number (4 strips)
+  //--------------------------------------------
+
+  double localPhi =
+      phi - (id*90.0 + 5.0);
+
+  int sector =
+      (int)(localPhi/(85.0/4.0));
+
+  if( sector < 0 ) sector = 0;
+  if( sector > 3 ) sector = 3;
+
+  chBk = ring;
+  chDn = sector;
+  chUp = sector;
+
+  zFrac = 0.0;
+
+  if(verbose){
+
+    printf("\nQQQ Hit\n");
+    printf(" ID     = %d\n", id);
+    printf(" Ring   = %d\n", ring);
+    printf(" Sector = %d\n", sector);
+    printf(" r      = %.2f mm\n", r);
+    printf(" phi    = %.2f deg\n", phi);
+
+    hitPos.Print();
+  }
+}
+/*s
+inline TVector3 QQQ::GetHitPosWithSigma(double sigmaY_mm, double sigmaZ_mm){
+
+  double phi = SNorml[id%numDet].Phi();
+
+  TVector3 haha = hitPos;
+  haha.RotateZ(-phi);
+
+  double y = haha.Y() + gRandom->Gaus(0, sigmaY_mm);
+  if( sigmaY_mm < 0 ){
+    double deltaW = width/4;
+    y = TMath::Floor((haha.Y()-deltaW)/deltaW)*deltaW + deltaW*1.5; // when ever land on each strip, set the position to be center of the strip.
+    if( y >= 25 ) y = 15;
+  }
+
+  double z = haha.Z() + gRandom->Gaus(0, sigmaZ_mm);
+  if( sigmaZ_mm < 0 ){
+    haha.Z();
+    double delta = length/4;
+    int sign = z > 0 ? 1 : -1;
+    z = TMath::Floor( (abs(z)-gap/2)/delta )*delta + 0.5 * delta + gap/2;
+    if( z >= 107.375 ) z = 88.625;
+    z = sign * z;
+  }
+
+  haha.SetY(y);
+  haha.SetZ(z);
+  haha.RotateZ(phi);
+
+  return haha;
+
+}*/
+
+
+inline void QQQ::CalQQQPos(unsigned short ID,
+                           unsigned short chUp,
+                           unsigned short chDown,
+                           unsigned short chBack,
+                           float eUp,
+                           float eDown){
+
+  hitPos.Clear();
+
+  if( ID > 3 ) return;
+  if( chBack > 31 ) return;
+  if( chDown > 3 ) return;
+
+  const double ringWidth =
+      (qqqR2 - qqqR1)/32.0;
+
+  double r =
+      qqqR1 + (chBack + 0.5)*ringWidth;
+
+  const double sectorWidth =
+      85.0/4.0;
+
+  double phiDeg =
+      ID*90.0 + 5.0 +
+      (chDown + 0.5)*sectorWidth;
+
+  double phi =
+      phiDeg * TMath::DegToRad();
+
+  hitPos.SetXYZ(
+      r*TMath::Cos(phi),
+      r*TMath::Sin(phi),
+      qqqZPos
+  );
+
+  id   = ID;
+  chBk = chBack;
+  chDn = chDown;
+  chUp = chUp;
+}
+
+#endif 

Armory/ClassSX3.h

@@ -57,8 +57,8 @@ private:
   const int numDet = 12;
   const float radius = 88;
   const float width = 40;
-  const float length = 75;
-  const float gap = 46;
+  const float length = 75; // 75
+  const float gap = 46; // 46
 
   short id; // -1 when no hit
   short chUp;

Armory/ClassTransfer.h

@@ -16,7 +16,6 @@
 #include "Isotope.h"
 
 class ReactionConfig{
-
 public:
 
   ReactionConfig(){}
@@ -47,9 +46,9 @@ public:
   std::vector<float> beamEx;        ///excitation_energy_of_A[MeV]
 
 
-  void SetReaction(int beamA, int beamZ,
-                   int targetA, int targetZ,
-                   int recoilA, int recoilZ, float beamEnergy_AMeV){
+  void SetReaction(int beamA, int beamZ, // projectile
+                   int targetA, int targetZ, // target
+                   int recoilA, int recoilZ, float beamEnergy_AMeV){ // light recoil, e.g. alpha
     this->beamA = beamA;
     this->beamZ = beamZ;
     this->targetA = targetA;
@@ -176,10 +175,10 @@ public:
   void SetA(int A, int Z, double Ex);
   void Seta(int A, int Z);
   void Setb(int A, int Z);
-  void SetB(int A, int Z);
+  void SetB(int A, int Z, double Ex);
   void SetIncidentEnergyAngle(double KEA, double theta, double phi);
-  void SetExA(double Ex);
-  void SetExB(double Ex);
+  void SetExA(double Ex); // excitation energy of A in MeV
+  void SetExB(double Ex); // excitation energy of B in MeV
   void SetReactionFromFile(string settingFile);
   
   TString GetReactionName();
@@ -246,8 +245,8 @@ TransferReaction::TransferReaction(){
    SetA(24, 12, 0);
    Seta(4,2);
    Setb(1,1);
-   SetB(27,13);
-   TA = 2.5;
+   SetB(27,13, 0);
+   TA = 2.5; // MeV/u
    T = TA * reaction.beamA;
    
    ExA = 0;
@@ -301,17 +300,19 @@ void TransferReaction::Setb(int A, int Z){
   isReady = false;
   isBSet = false;
 }
-void TransferReaction::SetB(int A, int Z){
+void TransferReaction::SetB(int A, int Z, double Ex = 0){
   Isotope temp (A, Z);
-  mB = temp.Mass;
+  double mB0 = temp.Mass;     // ground state mass
+  mB  = mB0;
   reaction.recoilHeavyA = A;
   reaction.recoilHeavyZ = Z;
   nameB = temp.Name;
+  ExB = Ex;
   isReady = false;
   isBSet = true;
 }
 
-void TransferReaction::SetIncidentEnergyAngle(double KEA, double theta, double phi){
+void TransferReaction::SetIncidentEnergyAngle(double KEA, double theta, double phi){ // KEA in MeV/u, theta and phi in degree
   this->TA = KEA;
   this->T = TA * reaction.beamA;
   this->thetaIN = theta;
@@ -390,7 +391,8 @@ void TransferReaction::CalReactionConstant(){
    beta = k / (mA + ExA + ma + T);
    gamma = 1 / TMath::Sqrt(1- beta * beta);   
    Etot = TMath::Sqrt(TMath::Power(mA + ExA + ma + T,2) - k * k);
-   p = TMath::Sqrt( (Etot*Etot - TMath::Power(mb + mB + ExB,2)) * (Etot*Etot - TMath::Power(mb - mB - ExB,2)) ) / 2 / Etot;
+   double mBtot = mB + ExB;
+   p = TMath::Sqrt( (Etot*Etot - TMath::Power(mb + mBtot,2)) * (Etot*Etot - TMath::Power(mb - mBtot,2)) ) / 2 / Etot;
    
    PA.SetXYZM(0, 0, k, mA + ExA);
    PA.RotateY(thetaIN);

Armory/HistPlotter.h

@@ -0,0 +1,414 @@
+#ifndef HISTPLOTTER_H
+#define HISTPLOTTER_H
+#include <TCanvas.h>
+#include <TROOT.h>
+#include <TSystem.h>
+#include <TStyle.h>
+#include <iostream>
+#include <TFile.h>
+#include <TMemFile.h>
+#include <TH1.h>
+#include <TH2.h>
+#include <TCutG.h>
+#include <signal.h>
+#include <cstdlib>
+#include <utility>
+#include <fstream>
+#include <sstream>
+#include <unordered_map>
+#include <set>
+#include <TGraphErrors.h>
+
+class HistPlotter {
+private:
+    long long barrier_count, barrier_limit; //meant to keep track of how often to call FillN() on histograms
+    enum {TFILE, TMEMFILE} filetype;
+    std::unordered_map<std::string,TObject*> oMap; //!< Maps std::string to all TH1, TH2 objects in the class
+    std::unordered_map<std::string,TObject*> cutsMap; //!< Maps std::string to TCutG objects held by the class
+    std::set<std::string> folderList; //!< List of all folder names used to nest objects
+    std::unordered_map<TObject*,std::string> foldersForObjects; //!< Map that returns the folder corresponding to the object whose pointer is specified
+    TFile *ofile=nullptr; //!< TFile pointer for the output file
+    TMemFile *omfile=nullptr; //!< TFile pointer for the output memfile
+
+    //Caches to permit FillN() calls
+    std::unordered_map<std::string, std::vector<double>> onedimcache;
+    std::unordered_map<std::string, std::pair<std::vector<double>, std::vector<double>>> twodimcache;
+    inline void FillN_All_Histograms();
+public:
+    HistPlotter(std::string outfile, std::string type);
+    inline void FlushToDisk(); //!< Writes all objects to file before closing, nesting objects in folders as is found necessary
+    inline void PrintObjects(); //!< Dump objects to std::cout for inspection
+    inline void ReadCuts(std::string); 
+    inline TCutG* FindCut(std::string cut) {
+        return static_cast<TCutG*>(cutsMap.at(cut));
+    }
+    inline void set_barrier_limit(long long limit) { barrier_limit = limit; }
+    inline void barrier_increment() {
+        barrier_count++;
+        if(barrier_count == barrier_limit) {
+            FillN_All_Histograms();
+            barrier_count=0;
+        }
+    }
+    /*! \fn void FindCut()
+        \brief        
+            - Searches for a cut by name 'cut' in the internal list of cuts 'cutsMap'. Ugly fails (via unresolved at()) if such a cut isn't found.            
+        \param filename - name of the plainxtext file containing the cut file locations and identifiers
+        \return Pointer to the TCutG object that matches the name. Very useful to use this as plotter.FindCut("protonbarrelpid")->IsInside(deltaE, E) for instance.
+    */
+
+    inline void SetNewTitle(std::string name, std::string title) {
+        auto result = oMap.find(name); //result is an iterator
+        if(result==oMap.end()) return; //no warnings, could be changed in future
+        else
+        	static_cast<TNamed*>(oMap.at(name))->SetTitle(title.c_str()); // set new title
+	}
+
+    //Smart functions that create a new histogram if it doesn't exist.
+    inline void FillGraph(const std::string &name, float valuex, float valuey, float errx=0, float erry=0);
+    inline void Fill1D(const std::string& name,int nbinsx, float xlow, float xhigh, float value);
+    inline void Fill2D(const std::string& name,int nbinsx, float xlow, float xhigh
+                ,int nbinsy, float ylow, float yhigh, float valuex, float valuey);
+    inline void Fill1D(const std::string& name,int nbinsx, float xlow, float xhigh, float value, const std::string& folder);
+    inline void Fill2D(const std::string& name,int nbinsx, float xlow, float xhigh
+                ,int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string& folder);
+    //TObject* findObject(std::string key);
+};
+
+HistPlotter::HistPlotter(std::string outfile, std::string type="") {
+    /*!
+        \brief Constructor. Opens a TFile instance with the specified filename
+        \param outfile : std::string that holds the desired output ROOT filename
+        \return None
+    */
+    if(type=="" || type == "TFILE") {
+        ofile = new TFile(outfile.c_str(),"recreate");
+        filetype = TFILE;
+    } else if(type =="TMEMFILE") {
+        omfile = new TMemFile(outfile.c_str(),"recreate");
+        filetype=TMEMFILE;
+    } else {
+        std::cout << "Unknown type "<< type << " specified for HistPlotter (use \"TFILE\" or \"TMEMFILE\"), using default \"TFILE\"  " << std::endl;
+        ofile = new TFile(outfile.c_str(),"recreate");
+        filetype = TFILE;
+    }
+    barrier_count=0;
+    barrier_limit=1000;
+}
+
+void HistPlotter::FillN_All_Histograms() {
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        //it->first is std::string 'name', it->second is the TObject
+        if(it->second->InheritsFrom("TH1F")) {
+            //FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size)
+            static_cast<TH1F*>(it->second)->FillN(onedimcache[it->first].size(), //size
+                                                  onedimcache[it->first].data(), //array
+                                                  std::vector<double>(onedimcache[it->first].size(),1.0).data()); //weight of ones
+            onedimcache[it->first].clear();
+        }  else if(it->second->InheritsFrom("TH2F")) {
+            //FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size))
+            static_cast<TH2F*>(it->second)->FillN(twodimcache[it->first].first.size(), //size
+                                                  twodimcache[it->first].first.data(), //x array
+                                                  twodimcache[it->first].second.data(), //y array
+                                                  std::vector<double>(twodimcache[it->first].first.size(),1.0).data()); //weight of ones
+           twodimcache[it->first].first.clear();
+           twodimcache[it->first].second.clear();
+        }
+    }
+    std::cout << "." << std::endl;
+}
+void HistPlotter::FlushToDisk() {
+    /*! \fn void FlushToDisk()
+        \brief         Function that can be used at any point to exit smoothly by saving all ROOT objects in memory
+        to the output file before closing it. Obeys the binding of histograms to separate folders, if so specified.
+        \return No return -- void
+    */
+    if(filetype==TMEMFILE && omfile) {
+        std::cout << "Not flushing a TMemfile .. exiting .." << std::endl;
+        delete omfile;
+        return;
+    }
+    if(ofile->IsZombie() || !ofile) {
+        std::cerr << "Output file is zombie, finishing up without writing to disk!" << std::endl;
+        return;
+    }
+    FillN_All_Histograms();
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        //omap maps: name(first) to object address(second).
+        // foldersForObjects maps: object address(first) to foldername(second)
+        auto result = foldersForObjects.find(it->second); //returns <TObject* histogram,std::string foldername> pair if found
+        if(result!=foldersForObjects.end()) { //we try to create folder if needed and cd to it
+            ofile->mkdir(result->second.c_str(),"",kTRUE); // args: name, title, returnExistingDirectory
+            ofile->cd(result->second.c_str());
+        } else {
+            ofile->cd(); //toplevel for all default histograms. Default setting
+        }
+        it->second->Write();
+    }
+
+    //Create a directory for all cuts, and save all cuts in them
+    ofile->mkdir("gCUTS","",kTRUE);
+    ofile->cd("gCUTS");
+    for(auto it=cutsMap.begin(); it!=cutsMap.end(); it++) {
+        (static_cast<TNamed*>(it->second))->SetName(it->first.c_str());
+        it->second->Write();
+    }
+    ofile->Close();
+    std::cout << "Wrote " << oMap.size() << " histograms to TFile " << std::string(ofile->GetName()) << std::endl;
+}
+
+void HistPlotter::FillGraph(const std::string& name, float valuex, float valuey, float errx, float erry) {
+    /*! \fn void FillGraph()
+        \brief
+        - Creates a TGraphError in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TGraph*
+
+        \param name name of the TGraph
+        \param valuex The xvalue
+        \param valuey The yvalue
+        \param errx The x error
+        \param erry The y error
+        \return No return void
+    */
+    auto result = oMap.find(name); 
+    if(result==oMap.end()) {
+        TGraphErrors *tempG = new TGraphErrors();
+        tempG->SetName(name.c_str());
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(tempG)));
+    }
+    if(!oMap.at(name)->InheritsFrom("TGraphErrors")) {
+        std::cerr << "Object " << name << " refers to something other than a TGraph*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    // static_cast<TGraphErrors*>(oMap.at(name))->AddPointError(valuex,valuey,errx,erry);
+}
+
+void HistPlotter::Fill1D(const std::string& name, int nbinsx, float xlow, float xhigh, float value) {
+    /*! \fn void Fill1D()
+        \brief  
+        - Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \return No return void
+    */
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH1F* temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+    } else if(foldersForObjects.find(oMap.at(name))!=foldersForObjects.end()) { //shouldn't have a folder associated with it
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH1F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    //static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill1D(const std::string& name, int nbinsx, float xlow, float xhigh, float value, const std::string& foldername) {
+    /*! \fn void Fill1D()
+        \brief        
+      -  Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not, defaults to toplevel.
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH1F* temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+        if(foldername!="") {
+            if(folderList.find(foldername)==folderList.end()) {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject*>(temp1D),foldername));
+        }
+    } else {
+        //object is present in map, but we enforce unique names
+        //it must already have a folder attached to it
+        if(foldersForObjects.find(oMap.at(name))==foldersForObjects.end()) {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        } else if(foldersForObjects[oMap[name]]!=foldername) {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH1F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    //static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill2D(const std::string& name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey) {
+    /*! \fn void Fill2D()
+        \brief        
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH2F* temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(),std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+    } else if(foldersForObjects.find(oMap.at(name))!=foldersForObjects.end()) { //shouldn't have a folder associated with it
+        std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH2F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    //static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::Fill2D(const std::string& name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string& foldername) {
+    /*! \fn void Fill2D()
+        \brief        
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not defaults to toplevel
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH2F* temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(),std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+        if(foldername!="") {
+            if(folderList.find(foldername)==folderList.end()) {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject*>(temp2D),foldername));
+        }
+    } else {
+        //object is present in map, but we enforce unique names
+        //it must already have a folder attached to it
+        if(foldersForObjects.find(oMap.at(name))==foldersForObjects.end()) {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        } else if(foldersForObjects[oMap.at(name)]!=foldername) {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH2F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    //static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::ReadCuts(std::string filename) {
+    /*! \fn void ReadCuts()
+        \brief  Reads a list of cuts from a file. The file must have the format below, two columns
+                   - Column#1 - path to a file that contains a single TCutG object named "CUTG", the default name in ROOT.
+                   - Column#2 - The identifier name you plan to use in the code, like 'protonbarrelpid' or something, that will be searched by FindCut()
+        \param filename name of the plainxtext file containing the cut file locations and identifiers
+        \return No return -- void
+    */
+
+    std::ifstream infile;
+    infile.open(filename);
+    std::string cutfilename, cutname;
+    for(std::string line; std::getline(infile, line); ) {
+        if(line.size()!=0 && line[0]=='#')
+            ; //don't do anything with '#' lines
+        else {
+            std::stringstream ss(line);
+            ss>>cutfilename>>cutname;
+
+            TFile f(cutfilename.c_str());
+            if(f.IsZombie()) {
+                std::cerr << "Cannot open cutfile " << cutfilename << " .. skipping.." << std::endl;
+                continue;
+            }
+            TCutG *cut = (TCutG*)(f.Get("CUTG"));
+            cutsMap.insert(std::make_pair(cutname,static_cast<TObject*>(cut)));
+            f.Close();
+        } //else
+    }//for loop
+    infile.close();
+}
+
+void HistPlotter::PrintObjects() {
+    /*
+        void PrintObjects()
+        Prints the contents of the unordered_maps oMap and cutsMap to facilitate debugging
+
+    */
+    std::cout << "Type | Name " << std::endl;
+    std::cout << "---- | --------------------- " << std::endl;
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        std::cout << it->second->ClassName() << " | "<< it->first << std::endl;
+    }
+    for(auto it=cutsMap.begin(); it!=cutsMap.end(); it++ ) {
+        std::cout << it->second->ClassName() << " | "<< it->first << std::endl;
+    }
+    std::cout << "---- | --------------------- " << std::endl;
+}
+
+#endif

Armory/Hit.h

@@ -0,0 +1,52 @@
+#ifndef Hit_H
+#define Hit_H
+
+#include <vector>
+
+class Hit{
+public:
+  unsigned short sn;
+  uint8_t ch;
+  unsigned short energy;
+  unsigned short energy2;
+  unsigned long long timestamp;
+  unsigned short fineTime;
+  bool pileUp;
+
+  unsigned short traceLength;
+  std::vector<short> trace;
+
+  Hit(){
+    Clear();
+  }
+
+  void Clear(){
+    sn = 0;
+    ch = 0;
+    energy = 0;
+    energy2 = 0;
+    timestamp = 0;
+    fineTime = 0;
+    traceLength = 0;
+    pileUp = false;
+    trace.clear();
+  }
+
+  void Print(){
+    printf("(%5d, %2d) %6d %16llu, %6d, %d, %5ld\n", sn, ch, energy, timestamp, fineTime, pileUp, trace.size());
+  }
+
+  void PrintTrace(){
+    for( unsigned short i = 0; i < traceLength; i++){
+      printf("%3u | %6d \n", i, trace[i]);
+    }
+  }
+
+  // Define operator< for sorting
+  bool operator<(const Hit& other) const {
+    return timestamp < other.timestamp;
+  }
+
+};
+
+#endif

Armory/LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
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+software and other kinds of works.
+
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+GNU General Public License for most of our software; it applies also to
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Armory/Makefile

@@ -1,28 +1,74 @@
 ########################################################################
-#
-#
-#########################################################################
+# Cross-platform Makefile (macOS + Linux)
+########################################################################
 
-CC	=	g++
+UNAME_S := $(shell uname -s)
 
-#COPTS	=	-fPIC -DLINUX -O2 -std=c++17 -lpthread
-COPTS	=	-fPIC -DLINUX -g -O0 -Wall -std=c++17 -lpthread
+########################################################################
+# Defaults
+########################################################################
 
-ROOTLIBS = `root-config --cflags --glibs`
+ifeq ($(UNAME_S),Darwin)
 
-ALL = Mapper AnasenMS
+########################################################################
+# macOS (Homebrew + Apple Clang)
+########################################################################
 
-#########################################################################
+SDKROOT := $(shell xcrun --show-sdk-path)
 
-all	:	$(ALL)
+CXX := clang++
 
-clean	:
-		/bin/rm -f $(OBJS) $(ALL)
+ROOTCFLAGS := $(shell root-config --cflags | sed 's/-stdlib=libc++//g')
+ROOTLIBS   := $(shell root-config --libs   | sed 's/-stdlib=libc++//g')
 
-Mapper	:	Mapper.cpp  ../mapping.h ClassDet.h
+CXXFLAGS := -g -O0 -Wall -std=c++17 -fPIC
+CXXFLAGS += $(ROOTCFLAGS)
+CXXFLAGS += -isysroot $(SDKROOT)
+CXXFLAGS += -I$(SDKROOT)/usr/include/c++/v1
+
+LDFLAGS := $(shell root-config --glibs) -lGeom -lEve -lGui
+
+else
+
+########################################################################
+# Linux (system g++)
+########################################################################
+
+CXX := g++
+
+COPTS := -fPIC -DLINUX -g -O0 -Wall -std=c++17 -pthread
+
+ROOTCFLAGS := $(shell root-config --cflags)
+ROOTLIBS   := $(shell root-config --libs)
+
+CXXFLAGS := $(COPTS) $(ROOTCFLAGS)
+LDFLAGS := $(ROOTLIBS) -lGeom -lEve -lGui
+
+endif
+
+########################################################################
+# Targets
+########################################################################
+
+ALL = Mapper EventBuilder AnasenMS
+
+all: $(ALL)
+
+clean:
+	/bin/rm -f $(ALL)
+
+########################################################################
+# Build rules
+########################################################################
+
+Mapper: Mapper.cpp ../mapping.h ClassDet.h
 	@echo "--------- making Mapper"
-		$(CC) $(COPTS) -o Mapper Mapper.cpp $(ROOTLIBS)
+	$(CXX) $(CXXFLAGS) Mapper.cpp -o Mapper $(LDFLAGS)
 
-AnasenMS : constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h anasenMS.cpp 
+EventBuilder: EventBuilder.cpp ClassData.h fsuReader.h Hit.h
+	@echo "--------- making EventBuilder"
+	$(CXX) $(CXXFLAGS) EventBuilder.cpp -o EventBuilder $(LDFLAGS)
+
+AnasenMS: anasenMS.cpp constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h
 	@echo "--------- making ANASEN Monte Carlo"
-		$(CC) $(COPTS) -o AnasenMS anasenMS.cpp $(ROOTLIBS)
+	$(CXX) $(CXXFLAGS) anasenMS.cpp -o AnasenMS $(LDFLAGS)

Armory/Mapper.dSYM/Contents/Info.plist

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<key>CFBundleIdentifier</key>
+		<string>com.apple.xcode.dsym.Mapper</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundlePackageType</key>
+		<string>dSYM</string>
+		<key>CFBundleSignature</key>
+		<string>????</string>
+		<key>CFBundleShortVersionString</key>
+		<string>1.0</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+	</dict>
+</plist>

Armory/Mapper.dSYM/Contents/Resources/Relocations/aarch64/Mapper.yml

@@ -0,0 +1,5 @@
+---
+triple:          'arm64-apple-darwin'
+binary-path:     Mapper
+relocations:     []
+...

Armory/README_anasenMS.md

@@ -0,0 +1,98 @@
+# ANASEN Monte Carlo (anasenMS.cpp)
+
+## Overview
+
+`anasenMS.cpp` is a standalone Monte Carlo simulation for an ANASEN-style detector setup. It generates transfer reaction kinematics, propagates products to a wire chamber (PW) and a silicon array (SX3), reconstructs tracks, and writes output to a ROOT tree.  
+
+## Requirements
+
+- ROOT (e.g. `root-config` for compile flags)
+- C++ compiler (gcc/g++)
+- Project includes: `ClassTransfer.h`, `ClassAnasen.h`, plus their dependent implementation files.
+
+## Build
+
+In `Armory` directory:
+
+the directory contains a make file
+
+Run `make AnasenMS` and it will automatically run
+
+```bash
+g++ -O2 -o anasenMS anasenMS.cpp ClassTransfer.cpp ClassAnasen.cpp ... `root-config --cflags --libs`
+```
+
+(Adjust source file list based on actual project layout.)
+
+## Run
+
+```bash
+./anasenMS [numEvents] vis(optional)
+```
+
+- `numEvents`: optional integer, default `1000000`
+- Outputs: `SimAnasen1.root` containing `tree1` and `tree2`
+tree1 contains pre-energy loss calculations
+tree2 contains post-energy loss calculations (subject to change)
+
+## What the code does
+
+- Detector geometry is built within ClassAnasen.h
+
+-To assign dead channels (anode/cathode/SX3), add ID's to IsDead<detector> boolean functions at top of simulation,
+  inside the set
+
+- Initializes reaction: `TransferReaction transfer`
+  - `SetA(24,12,0)` target
+  - `SetIncidentEnergyAngle(10,0,0)` beam energy and direction
+  - `Seta`, `Setb` reaction fragment indices
+- Sets excitation lists: `ExAList`, `ExList`
+- Vertex and resolution settings:
+  - `vertexX/Y/Z` ranges
+  - `sigmaSX3_W`, `sigmaSX3_L`, `sigmaPW_A`, `sigmaPW_C`
+- Loads energy loss tables from `../ELoss/` using `TGraph` for interpolation
+- Prepares ROOT output tree and branches for truth/reconstructed
+- Loop over events:
+  - Sample excitation and CM direction
+  - `transfer.Event(thetaCM, phiCM)` outputs `TLorentzVector` products
+  - Compute lab angles/energies
+  - Random vertex inside target volume
+  - Run detector response:
+    - `pw->FindWireID(...)`
+    - `sx3->FindSX3Pos(...)`
+  - Read out wire hits and SX3 channel + depth
+  - Apply position smearing for SX3
+  - **Apply energy loss** to light particle using interpolated dE/dx from table, based on path length from vertex to hit
+  - Reconstruct track via `pw->CalTrack` and `pw->CalTrack2`
+  - Fill ROOT tree
+- At end: write tree, close file, clean up
+
+## Notes
+
+- Important methods are from:
+  - `ClassTransfer` (`SetA`, `SetIncidentEnergyAngle`, `Seta`, `Setb`, `SetExA`, `SetExB`, `CalReactionConstant`, `Event`)
+  - `ClassAnasen` / `SX3` / `PW` (`FindWireID`, `FindSX3Pos`, `GetHitInfo`, `CalTrack`, `CalTrack2`, `GetTrackTheta`, `GetTrackPhi`, `GetZ0`, `GetHitPosWithSigma`, `GetID`, etc.)
+- Optional: change excitation lists, vertex spread, and sigma values to mimic different beam/target conditions.
+
+## Example Workflow
+
+- Say you want to do a beam of Al27 through standard pressure gas.
+  - If using the random energy scan route, determine the depth your beam travels in the detector, and set the appropriate window in the .cpp file in <<vertexZRange>>.
+  - If you want to track it's energy loss through the detector, create a lookup table with PCEnergyAnalysis.py in the helium and import it using <<elossbeam>>. When making the table, set the initial energy of the beam as the 'max energy' of the table.
+To take into account things like the kapton window and other materials, make lookup tables for them and map their energy loss through them one after another, and use the final energy from that as the maximum beam energy.
+
+- For there you need to run a simulation for each reaction you want to measure. Declare their components in the transfer.Set(A,a,b,B). A is your beam, a is the helium target, b is your proton, alpha, deuterium, etc, and B is the daughter nuclei. 
+
+- Run 'make AnasenMS' in the build directory and let it compile. From there, run the excecutable './AnasenMS'. The simulation will run and automatically load all the data into the root file 'SimAnasen1.root'. This is the file that gets read into PCEnergyAnalysis.py. 
+
+- Once the simulation is complete, start the analysis script. Do not start it while the simulation is still running, or you will miss data. The simulation will automatically open the file SimAnasen1.root, and with that you can run 'make_plots'. If it's proton data, it will assume that automatically, but if it is alpha data, you need to pass 'alpha' as an additional argument.
+
+- If you have two reactions to analyze, you can use 'dual_plotter'. Renaming them 'SimAnasenProton.root' and 'SimAnasenAlpha.root' will allow you to run the function with no additional arguments. However, for any other names or additional reactions, you will need to add the file names manually as additional arguments. The program assumes them to be in the Armory directory, so if they are in a subfile, include the subfile in the argument. 
+
+- Plots and histograms will automatically get saved to the ELoss folder. By default reactions are on tree1, and are sorted by particle
+
+- Tree2 is used for secondary decay channels, and simulating double-proton decays. The secondary decay data is stored in tree2. Dual plotter will combine trees automatically, but make_plots assumes to use tree1. This can be switched using set_tree in the program, and then running make_plots
+  - Secondary reactions can be turned off and on with a boolean <<enableSequentialDecay>>
+  - Fill in relevant data about the decay in the lines following
+
+- Additional features include terminal energy loss calculations using initial energy, final energy and distance travelled. Using two of these three there are three different functions to find the third variable. For range, use energy_distance, declare the particle, medium, the initial energy, and set final energy to 0. This will give you the range of the given particle. 

Armory/SX3Geom.h

@@ -0,0 +1,183 @@
+#ifndef SX3Geom_h
+#define SX3Geom_h
+#include <vector>
+
+const double DEFAULT_NULL=-987654321.;
+
+class sx3_geometry_scalefactors {
+public:
+    //If sx3 has L, R being the left and right extremities, we choose add, stretch here such that
+    // x_mm = (x_raw+add)*stretch; so add=abs(L), stretch=75/(abs(L)+R)
+    float add[4];
+    float stretch[4];
+};
+
+class qqq5_finegains {
+public:
+    std::array<std::pair<float,float>,32> front;
+    //front.at(30).first = slope at clkpos 0, ring 30 for E front layer
+    //front.at(30).second = intercept for the same as above
+    std::array<std::pair<float,float>,4> back;
+};
+class sx3_fbgains {
+public:
+    //Order of indices is [pad][strip]
+    float padoffsets[4][4];
+    float padgains[4][4];
+
+    float stripLoffsets[4][4];
+    float stripLgains[4][4];
+
+    float stripRoffsets[4][4];
+    float stripRgains[4][4];
+};
+
+std::array<sx3_fbgains,24> sx3_xtalk_gains; //every sx3 needs to be gainmatched as a frontL-back, frontR-back pair (pad strip pair)
+std::array<sx3_geometry_scalefactors,24> sx3gs;
+
+class sx3 {
+public:
+    //TODO: Convert to std::array
+    //Holds all information in an event, including ped subtraction+scaling. back[2].at(0) will have the largest energy seen in ch2, if any
+    std::vector<float> back[4];
+    std::vector<float> frontL[4];
+    std::vector<float> frontR[4];
+
+    double ts = DEFAULT_NULL;
+    //Easy lookup of final calibrated event. Only filled for valid cases, assumed for now to be 1L, 1R, 1B
+    float frontX=DEFAULT_NULL;
+    float frontXmm=DEFAULT_NULL;
+    float frontE=DEFAULT_NULL;
+    float backE=DEFAULT_NULL;
+    int stripF=DEFAULT_NULL;
+    int stripB=DEFAULT_NULL;
+    float frontEL=DEFAULT_NULL;
+    float frontER=DEFAULT_NULL;
+
+    float phi=DEFAULT_NULL; //
+
+    std::set<int> valid_front_chans;
+    std::set<int> valid_back_chans;
+    std::set<int> unmatched_front_chans; //every front channel is unmatched and invalid at first. when it gets matched, it gets removed and sent to valid
+
+    bool foundevent=false;
+    bool valid=false;//valid will be set to false in all cases where we have ambiguity
+    int flags=-1;//flags settable to different types of values to indicate different invalid situations
+
+    void fillevent(const std::string& position, const int subchannel, const float value); //make 'const' what functions don't need to change, helps with performance
+    void validate(const sx3_fbgains&, const sx3_geometry_scalefactors&);
+    void validate();
+};
+
+
+void sx3::fillevent(const std::string& positionstring, const int subchannel, const float value) {
+    assert(subchannel>=0 && subchannel<4);
+    if(positionstring=="FRONT_L") {
+        frontL[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="FRONT_R") {
+        frontR[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="BACK") {
+        back[subchannel].push_back(value);
+        valid_back_chans.insert(subchannel);
+    } else {
+        std::cout << "Unknown string "+positionstring+" encountered in sx3::fillevent \n" << std::endl;
+    }
+    if(frontL[subchannel].size()!=0 && frontR[subchannel].size()!=0 ) {
+        unmatched_front_chans.erase(subchannel);
+        valid_front_chans.insert(subchannel); //std::set, so no duplication will happen
+    }
+}
+
+
+//void sx3::validate(const sx3_fbgains& fbgains, const sx3_geometry_scalefactors& sx3gs) {
+void sx3::validate() {
+    if(valid_front_chans.size()!=0 && valid_back_chans.size()!=0) {
+        valid=true;
+        float maxFE=0;
+        float maxBE=0;
+        //float zpos=0;
+        int bchan=-1;
+        int fchan=-1;
+/*            	for(auto cc: valid_front_chans) {
+            		std::cout << "fc" << cc << std::endl;// " " << frontL[cc].at(0) << " " << frontR[cc].at(0) << std::endl;
+            	}
+            	for(auto cc: valid_back_chans) {
+            		std::cout << "bc" << cc << std::endl; //" " << back[cc].at(0) << std::endl;
+            	}
+*/
+        for(auto chan: valid_front_chans) {
+            if(frontL[chan].size()>1) {
+                printf("\nmultihit sx3 at Lsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontL[chan]) printf("e: %f\t",e);
+                std::sort(frontL[chan].begin(), frontL[chan].end(), std::greater<float>());
+                flags += (-1000);
+            }
+            if(frontR[chan].size()>1) {
+                printf("\nmultihit sx3 at Rsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontR[chan]) printf("e: %f\t",e);
+                std::sort(frontR[chan].begin(), frontR[chan].end(), std::greater<float>());
+                flags += (-2000);
+            }
+            //assign position using max L+R value
+            /*printf("chan:%d sizeL: %d sizeR: %d\n",chan, frontL[chan].size(), frontR[chan].size()); fflush(stdout);
+			printf("foo\n");
+			std::cout << "\nL:" << std::endl;
+			for(auto thing: frontL[chan]) std::cout << thing << " " << std::flush;
+			std::cout << "\nR:" << std::endl;
+			for(auto thing: frontR[chan]) std::cout << thing << " " << std::flush;*/
+            if(frontL[chan].at(0) + frontR[chan].at(0)> maxFE) {
+                maxFE = frontL[chan].at(0) + frontR[chan].at(0);
+                //zpos = (frontL[chan].at(0)-frontR[chan].at(0))/maxFE;
+                fchan = chan;
+            }
+        }
+        for(auto chan: valid_back_chans) {
+            if(back[chan].size()>1) {
+                printf("\nmultihit sx3 at Bsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: back[chan]) printf("e: %f\t",e);
+                std::sort(back[chan].begin(), back[chan].end(), std::greater<float>());
+                flags += (-3000);
+            }
+            if(back[chan].size() ==0 ) {
+            	printf("foo\n");
+            	//continue;
+            }
+            if(back[chan].at(0) > maxBE) {
+                maxBE = back[chan].at(0);
+                bchan = chan;
+            }
+        }
+        /*
+        	Cross-talk corrections are important when evaluating 'energy' signals from strips/pads.
+        	They can cause unexpected behavior when used universally for all EL, ER cases, so we split scenarios in two.
+        		- Positions along each strip (frontX) *are not* corrected for crosstalk.
+        		- Total F and B energies (frontE, backE) *are*.
+        	Sudarsan B, 31 Oct 2024
+        */
+        float Eleft = frontL[fchan].at(0);
+        float Eright = frontR[fchan].at(0);
+        frontEL = Eleft;
+        frontER = Eright;
+        frontX = (Eleft-Eright)/(Eleft+Eright);
+        //frontXmm = (frontX+sx3gs.add[fchan])*sx3gs.stretch[fchan]; //convert to mm
+
+        //frontE = Eleft*fbgains.stripLgains[bchan][fchan] + fbgains.stripLoffsets[bchan][fchan]
+         //        + Eright*fbgains.stripRgains[bchan][fchan]  + fbgains.stripRoffsets[bchan][fchan];
+        //backE = back[bchan].at(0)*fbgains.padgains[bchan][fchan]+fbgains.padoffsets[bchan][fchan];
+        frontE = Eleft+Eright;
+        backE = maxBE;
+        stripF=fchan;
+        stripB=bchan;
+
+        flags = 0;
+    } else if(valid_front_chans.size()!=0 && valid_back_chans.size()==0) {
+        flags = -10;
+    } else if(valid_front_chans.size()==0 && valid_back_chans.size()!=0) {
+        flags = -20;
+    }
+}
+
+typedef sx3 sx3det;
+#endif

Armory/TrainingBuilder.py

@@ -0,0 +1,180 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Train a TensorFlow model from a directory of ROOT files.
+
+Inputs:
+    Tb
+    thetab
+    vZ
+    MBeam
+    MTarget
+    MLight
+    MHeavy
+
+Outputs:
+    beamEnergy
+    Ex
+"""
+import numpy as np
+from pathlib import Path
+
+import joblib
+import pandas as pd
+import uproot
+
+from sklearn.model_selection import train_test_split
+from sklearn.preprocessing import StandardScaler
+
+import tensorflow as tf
+from tensorflow.keras import Sequential
+from tensorflow.keras.layers import Dense
+from tensorflow.keras.callbacks import EarlyStopping
+
+ROOT_FOLDER = Path("/Users/jamesszalkie/ANASEN_analysis/Armory/Training_Data_Ne/")
+
+TREE_NAME = "tree1"
+
+INPUT_BRANCHES = [
+    "Tb",
+    "thetab",
+    "vZ",
+    "MBeam",
+    "MTarget",
+    "MLight",
+    "MHeavy",
+]
+
+OUTPUT_BRANCHES = [
+    "beamEnergy",
+    "Ex",
+]
+
+MODEL_NAME = "beam_predictor.keras"
+
+print("Reading ROOT files...")
+
+dfs = []
+
+for root_file in sorted(ROOT_FOLDER.glob("*.root")):
+
+    print(f"  {root_file.name}")
+
+    with uproot.open(root_file) as f:
+
+        tree = f[TREE_NAME]
+
+        arrays = tree.arrays(
+            INPUT_BRANCHES + OUTPUT_BRANCHES,
+            library="np"
+        )
+
+        dfs.append(pd.DataFrame(arrays))
+
+dataset = pd.concat(dfs, ignore_index=True)
+
+# Remove events with missing or invalid values
+dataset = dataset.replace([np.inf, -np.inf], np.nan)
+dataset = dataset.dropna()
+
+print(f"Training on {len(dataset)} complete events.")
+
+print(dataset.describe())
+
+print()
+
+print(dataset.isna().sum())
+
+print()
+
+print(np.isinf(dataset).sum())
+
+print()
+print("Total events:", len(dataset))
+
+X = dataset[INPUT_BRANCHES].values
+Y = dataset[OUTPUT_BRANCHES].values
+
+X_train, X_test, Y_train, Y_test = train_test_split(
+    X,
+    Y,
+    test_size=0.20,
+    random_state=42,
+)
+
+input_scaler = StandardScaler()
+output_scaler = StandardScaler()
+
+X_train = input_scaler.fit_transform(X_train)
+X_test = input_scaler.transform(X_test)
+
+Y_train = output_scaler.fit_transform(Y_train)
+Y_test = output_scaler.transform(Y_test)
+
+model = Sequential([
+    Dense(128, activation="relu"),
+    Dense(128, activation="relu"),
+    Dense(64, activation="relu"),
+    Dense(32, activation="relu"),
+    Dense(2)
+])
+
+model.build((None, len(INPUT_BRANCHES)))
+
+model.compile(
+    optimizer="adam",
+    loss="mse",
+    metrics=["mae"]
+)
+
+model.summary()
+
+early_stop = EarlyStopping(
+    monitor="val_loss",
+    patience=20,
+    restore_best_weights=True
+)
+
+history = model.fit(
+    X_train,
+    Y_train,
+    epochs=25,
+    batch_size=512,
+    validation_split=0.20,
+    callbacks=[early_stop],
+    verbose=1,
+)
+
+loss, mae = model.evaluate(
+    X_test,
+    Y_test,
+    verbose=0,
+)
+
+pred_scaled = model.predict(X_test, verbose=0)
+
+pred = output_scaler.inverse_transform(pred_scaled)
+truth = output_scaler.inverse_transform(Y_test)
+
+print()
+print(f"Test Loss : {loss:.6f}")
+print(f"Test MAE  : {mae:.6f}")
+
+beam_error = np.mean(np.abs(pred[:,0] - truth[:,0]))
+Ex_error = np.mean(np.abs(pred[:,1] - truth[:,1]))
+
+print(f"Beam Energy MAE: {beam_error:.6f} MeV")
+print(f"Ex MAE: {Ex_error:.6f} MeV")
+
+model.save(MODEL_NAME)
+
+joblib.dump(input_scaler, "input_scaler.pkl")
+joblib.dump(output_scaler, "output_scaler.pkl")
+
+print()
+print("Training complete.")
+print("Saved:")
+print("   ", MODEL_NAME)
+print("    input_scaler.pkl")
+print("    output_scaler.pkl")

Armory/aarootscript.C

@@ -0,0 +1,134 @@
+#include "TFile.h"
+#include "TTree.h"
+#include "TGraph.h"
+#include "TLegend.h"
+#include "TCanvas.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
+
+void aarootscript(int argument = 0) {
+    std::cout << "\n\n\n";
+    std::cout << "=========================================\n";
+    std::cout << "=========   ANASEN Root Script  =========\n";
+    std::cout << "=========================================\n";
+
+    TFile *f = new TFile("SimAnasen1.root");
+    TTree *tree1 = (TTree*)f->Get("tree");
+    if (!tree1) {
+        std::cerr << "Error: tree1 not found in the file!" << std::endl;
+        return;
+    }
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    TTreeReader reader("tree");
+    TTreeReaderValue<double> Tb1(reader, "Tb"); // this line will read the "Tb" branch from the tree and save it as 
+    TTreeReaderValue<double> TB1(reader, "TB"); // this line will read the "TB" branch from the tree and save it as Tb1
+    //add Tb1 and TB1 together 
+
+    double totalSum = 0;
+    while (reader.Next()) {
+        totalSum += *Tb1;
+    }
+    std::cout << "Total Sum: " << totalSum << std::endl;
+
+    TTreeReader reader2("tree2");
+    TTreeReaderValue<double> Tb2(reader2, "Tb");
+    double totalSum2 = 0;
+    int zeroCount = 0;
+    while (reader2.Next()) {
+        totalSum2 += *Tb2;
+        if (*Tb2 == 0) {
+            zeroCount++;
+        }
+    }
+    std::cout << "Total Sum: " << totalSum2 << std::endl;
+
+    std::cout << "Difference: " << totalSum - totalSum2 << std::endl;
+
+    std::cout << "Zero Count: " << zeroCount << std::endl;
+
+
+
+    //std::cout << "Making histograms..." << std::endl;
+
+    gErrorIgnoreLevel = 2001;
+    gROOT->ProcessLine(".x histcomp.C"); 
+
+    std::cout << "=========================================\n";
+
+    if (argument == 1) {
+        if (tree1) {
+            gROOT->ProcessLine("tree->Print();");
+        } else {
+            std::cout << "Tree1 not found!" << std::endl;
+        }
+    }
+
+    if (argument == 2) {
+        if (tree2) {
+            gROOT->ProcessLine("tree2->Print();");
+        } else {
+            std::cout << "Tree2 not found!" << std::endl;
+        }
+    }
+
+    std::cout << "Creating Tb vs dEb plot..." << std::endl;
+
+    // Readers for both trees
+    TTreeReader r1(tree1);
+    TTreeReader r2(tree2);
+
+    TTreeReaderValue<double> Tb_val(r1, "Tb");
+    TTreeReaderValue<double> TB_val(r2, "TB");
+    TTreeReaderValue<double> dEb_val(r2, "dEb");
+
+    std::vector<double> x; // Tb (tree1)
+    std::vector<double> y; // dEb (tree2)
+
+
+    // Loop over both trees simultaneously
+    while (r1.Next() && r2.Next()) {
+        x.push_back(*Tb_val);
+        y.push_back(*dEb_val);
+    }
+    std::cout << "x length: " << x.size() << ", y length: " << y.size() << std::endl;
+
+    std::ofstream outfile("Tb_dEb_data.txt");
+
+    if (!outfile.is_open()) {
+        std::cerr << "Error: Could not open output file!" << std::endl;
+        return;
+    }
+
+    for (size_t i = 0; i < x.size(); i++) {
+        outfile << x[i] << " " << y[i] << "\n";
+    }
+
+    outfile.close();
+
+    std::cout << "Data written to Tb_dEb_data.txt" << std::endl;
+    /*
+    // Create graph
+    TGraph *gr = new TGraph(x.size(), &x[0], &y[0]);
+    gr->SetTitle("Tb (tree1) vs dEb (tree2);Tb;dEb");
+    gr->SetMarkerStyle(20);
+
+    // Draw
+    TCanvas *c1 = new TCanvas("c1", "Tb vs dEb", 800, 600);
+    gr->Draw("AP");
+    c1->Update();
+    c1->SaveAs("Tb_vs_dEb.png");
+    std::cout << "Plot saved as Tb_vs_dEb.pdf" << std::endl;
+    std::cout << "\n\n\n";
+
+    delete c1;
+    delete gr;*/
+
+
+
+
+}
+

Armory/analyze.C

@@ -0,0 +1,111 @@
+#include "TFile.h"
+#include "TTree.h"
+#include "TCanvas.h"
+#include "TH1D.h"
+#include "TLegend.h"
+#include "TString.h"
+#include "TStyle.h"
+#include <iostream>
+
+void analyze(const char* filename = "SimAnasen1.root")
+{
+    gStyle->SetOptStat(1);
+
+    TFile *f = TFile::Open(filename);
+    if (!f || f->IsZombie()) {
+        std::cerr << "ERROR: cannot open file " << filename << std::endl;
+        return;
+    }
+
+    TTree *tree = (TTree*)f->Get("tree");
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    if (!tree) {
+        std::cerr << "ERROR: tree not found\n";
+        return;
+    }
+
+    std::cout << "\n===== BASIC TREE INFO =====\n";
+    tree->Print();
+
+    // Event inspection tools
+    std::cout << "\n===== FIRST 10 EVENTS =====\n";
+    tree->Scan("Tb:TB:anodeID[0]:cathodeID[0]:sx3ID", "", "", 10);
+
+    std::cout << "\n===== SINGLE EVENT EXAMPLE (0) =====\n";
+    tree->Show(0);
+
+    // Quick detector gating examples
+    std::cout << "\n===== GATED STATS =====\n";
+    std::cout << "Events with anodeID[0]==5: "
+              << tree->GetEntries("anodeID[0]==5") << std::endl;
+
+    std::cout << "Events with sx3ID>=0: "
+              << tree->GetEntries("sx3ID>=0") << std::endl;
+
+    // Tb vs TB comparison histogram
+
+    TCanvas *c1 = new TCanvas("c1","Tb vs TB",800,600);
+    //set min and max from tree values
+    double min = tree->GetMinimum("Tb");
+    double max = tree->GetMaximum("TB");
+    min = min - max*0.1;
+    max = max * 1.1;
+    TH1D *hTb = new TH1D("hTb","Tb and TB;Energy (MeV);Counts",200,min,max); //arguments are name, title (with axis labels), number of bins, x-min, x-max
+    TH1D *hTB = new TH1D("hTB","",200,min,max);
+
+    tree->Draw("Tb>>hTb","","goff");
+    tree->Draw("TB>>hTB","","goff");
+
+    hTb->SetLineColor(kRed);
+    hTB->SetLineColor(kBlue);
+
+    hTb->Draw("HIST");
+    hTB->Draw("HIST SAME");
+
+    TLegend *leg = new TLegend(0.65,0.75,0.88,0.88);
+    leg->AddEntry(hTb,"Tb (light)","l");
+    leg->AddEntry(hTB,"TB (heavy)","l");
+    leg->Draw();
+
+    c1->SaveAs("Tb_TB_compare.png");
+
+    // 4. Detector-gated histogram
+
+    TCanvas *c2 = new TCanvas("c2","Anode gated Tb",800,600);
+    double min2 = tree->GetMinimum("Tb");
+    double max2 = tree->GetMaximum("Tb");
+    min2 = min2 - max2*0.1;
+    max2 = max2 * 1.1;
+    TH1D *hGate = new TH1D("hGate","Tb (anodeID[0]==5);Energy;Counts",200,min2,max2);
+
+    tree->Draw("Tb>>hGate","anodeID[0]==5","goff");
+
+    hGate->SetLineColor(kGreen+2);
+    hGate->Draw("HIST");
+
+    c2->SaveAs("Tb_anode5.png");
+
+    // Tb vs TB correlation (with gate)
+
+    TCanvas *c3 = new TCanvas("c3","dEb vs SX3z",800,600);
+
+    tree->Draw("TB:Tb>>h2(200,min,max,200,min,max)","","COLZ"); //arguments are "y:x>>histogram(bins,xmin,xmax,bins,ymin,ymax)", "selection", "options"
+
+    c3->SaveAs("Tb_vs_TB.png");
+
+    // Make gated trees 
+
+    TFile *out = new TFile("gated_output.root","RECREATE");
+
+    TTree *t_anode5 = tree->CopyTree("anodeID[0]==5");
+    t_anode5->Write("tree_anode5");
+
+    TTree *t_sx3valid = tree->CopyTree("sx3ID>=0");
+    t_sx3valid->Write("tree_sx3valid");
+
+    out->Close();
+
+    std::cout << "\n===== DONE =====\n";
+    std::cout << "Saved plots + gated trees in gated_output.root\n";
+}

Armory/anasenMS Decay Version.cpp

@@ -0,0 +1,632 @@
+#include "TRandom.h"      // ROOT random number generators, gRandom
+#include "TFile.h"        // ROOT file I/O
+#include "TTree.h"        // ROOT tree storage
+#include "TH1.h"          // 1D histograms
+#include "TH2.h"          // 2D histograms
+#include "TStyle.h"       // ROOT plotting style controls
+#include "TCanvas.h"      // ROOT canvas drawing
+#include "TBenchmark.h"   // timing measurement
+#include "TGraph.h"       // for energy loss interpolation
+#include <cstring>
+#include "TApplication.h" // ROOT app loop
+#include "ClassTransfer.h" // Reaction kinematics and MC event generation
+#include "ClassAnasen.h"   // ANASEN detector model classes (SX3, PW, etc.)
+#include <stdio.h>
+#include <stdlib.h>
+#include <set>
+#include "TLegend.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
+
+//======== Generate light particle based on reaction
+// calculate real and reconstructed tracks and Q-value uncertainty
+
+// Function to load energy loss table from file
+TGraph* LoadELoss(const char* filename) {
+  TGraph* g = new TGraph(filename, "%lg %lg");
+  return g;
+}
+
+bool IsDeadAnode(int id){
+    static std::set<int> dead = {}; // add dead anode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadCathode(int id){
+    static std::set<int> dead = {}; // add dead cathode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadSX3(int id){ 
+    static std::set<int> dead = {}; // add dead SX3 IDs here, 0-23 1,7,9,3
+    return dead.count(id);
+}
+
+// Simulate sequential two-body decay of an unstable parent in its rest frame.
+// The parent is boosted from the lab frame, the daughter (A1,Z1) is returned in lab frame,
+// and the emitted ejectile (A2,Z2) is written to ejectileOut.
+TLorentzVector SimulateSequentialDecay(const TLorentzVector &parent,
+                                       int daughterA, int daughterZ,
+                                       int ejectA, int ejectZ,
+                                       TLorentzVector &ejectileOut){
+  Isotope daughter(daughterA, daughterZ);
+  Isotope ejectile(ejectA, ejectZ);
+
+  double M = parent.M();
+  double mD = daughter.Mass;
+  double mE = ejectile.Mass;
+
+  double sqM = M * M;
+  double sum = mD + mE;
+  double diff = mD - mE;
+  double p2 = (sqM - sum*sum) * (sqM - diff*diff) / (4.0 * sqM);
+  if( p2 < 0 ) p2 = 0;
+  double p = TMath::Sqrt(p2);
+
+  double cosTheta = 2.0 * gRandom->Rndm() - 1.0;
+  double theta = TMath::ACos(cosTheta);
+  double phi = gRandom->Rndm() * TMath::TwoPi();
+
+  TVector3 v;
+  v.SetMagThetaPhi(p, theta, phi);
+
+  TLorentzVector daughterLab;
+  daughterLab.SetVectM(v, mD);
+
+  TLorentzVector ejectileLab;
+  ejectileLab.SetVectM(-v, mE);
+
+  TVector3 boost = parent.BoostVector();
+  daughterLab.Boost(boost);
+  ejectileLab.Boost(boost);
+
+  ejectileOut = ejectileLab;
+  return daughterLab;
+}
+
+int main(int argc, char **argv){
+
+  printf("=========================================\n");
+  printf("===       ANASEN Monte Carlo          ===\n");
+  printf("=========================================\n");
+
+  // number of events can be overridden from command line
+  int numEvent = 1000000;
+  if( argc >= 2 ) numEvent = atoi(argv[1]);
+
+  // Reaction setup for 18Ne + 4He -> p + 21Na*.
+  // The heavy product 21Na* is then decayed to 20Ne + p in the simulation.
+  TransferReaction transfer;
+
+  transfer.SetA(18, 10, 0);            // 18Ne
+  transfer.SetIncidentEnergyAngle(4.4, 0, 0); // KEA in MeV/u, theta and phi in degree
+  transfer.Seta(4, 2);                 // 4He target
+  transfer.Setb(1, 1);                 // outgoing proton from the primary transfer
+  transfer.SetB(21, 11);               // 21Na* heavy product
+
+  bool enableSequentialDecay = true;
+  const int decayDaughterA = 20;
+  const int decayDaughterZ = 10;
+  const int decayEjectA = 1;
+  const int decayEjectZ = 1;
+
+  // Excited state lists (projectile and heavy-product excitation states)
+  std::vector<float> ExAList = {0};              // 18Ne projectile excitations in MeV
+  std::vector<float> ExList = {2.5};             // 21Na* excitation in MeV (above proton separation threshold)
+
+  // define vertex position uniform distribution ranges (mm)
+  double vertexXRange[2] = {   -5,    5}; // mm
+  double vertexYRange[2] = {   -5,    5};
+  double vertexZRange[2] = { -100,  100};
+
+  // detector resolution / uncertainty parameters
+  double sigmaSX3_W = -1; // mm, if < 0 use mid-point (no spread in SX3 horizontal dimension)
+  double sigmaSX3_L = 3;  // mm, vertical spread for SX3
+  double sigmaPW_A  = 0;  // normalized anode uncertainty term (0-1)
+  double sigmaPW_C  = 0;  // normalized cathode uncertainty term (0-1)
+
+  // status printout
+  printf("------------ Vertex :\n");
+  printf("X : %7.2f - %7.2f mm\n", vertexXRange[0], vertexXRange[1]);
+  printf("Y : %7.2f - %7.2f mm\n", vertexYRange[0], vertexYRange[1]);
+  printf("Z : %7.2f - %7.2f mm\n", vertexZRange[0], vertexZRange[1]);
+  printf("------------ Uncertainty :\n");
+  printf(" SX3 horizontal : %.1f\n", sigmaSX3_W);
+  printf(" SX3   vertical : %.1f\n", sigmaSX3_L);
+  printf("          Anode : %.1f mm\n", sigmaPW_A);
+  printf("        Cathode : %.1f mm\n", sigmaPW_C);
+  printf("        num_eve : %d \n",numEvent);
+
+  // calculates energy/momentum/kinematics constants for transfer reaction
+  transfer.CalReactionConstant();
+  printf("Primary reaction: %s at %.2f MeV/u\n", transfer.GetReactionName().Data(), 4.4);
+  printf("Sequential decay enabled: %s\n", enableSequentialDecay ? "yes" : "no");
+
+  int nExA = ExAList.size();
+  int nEx  = ExList.size();
+
+  // optional visualization control: pass "vis" as 3rd arg
+  bool enableVis = (argc >= 3 && strcmp(argv[2], "vis") == 0);
+  TApplication *app = nullptr;
+  if(enableVis){
+    app = new TApplication("anasenVis", &argc, argv);
+  }
+
+  // storage for tracks during simulation (for visualization)
+  std::vector<TVector3> visTrackVertex, visTrackDir, visTrackHitPos;
+  std::vector<std::pair<int,int>> visTrackWires;  // {anodeID, cathodeID}
+
+  // create detector representation in memory
+  ANASEN * anasen = new ANASEN();       // top-level detector object
+  SX3 * sx3 = anasen->GetSX3();         // silicon array part
+  PW * pw = anasen->GetPW();            // proportional wire chamber part
+
+  // output file + trees
+  TString saveFileName = "SimAnasen1.root";
+  printf("\e[32m#################################### building Tree in %s\e[0m\n", saveFileName.Data());
+  TFile * saveFile = new TFile(saveFileName, "recreate");
+  TTree * tree1 = new TTree("tree1", "tree1");
+  TTree * tree2 = new TTree("tree2", "tree2");
+
+  // beam and CM variables saved in tree
+  double KEA;
+  double KEA2;
+  tree1->Branch("beamKEA",     &KEA, "beamKEA/D");
+  tree2->Branch("beamKEA",     &KEA2, "beamKEA/D");
+
+  double thetaCM, phiCM;
+  double thetaCM2, phiCM2;
+  tree1->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  tree1->Branch("phiCM",     &phiCM, "phiCM/D");
+  tree2->Branch("thetaCM", &thetaCM2, "thetaCM/D");
+  tree2->Branch("phiCM",     &phiCM2, "phiCM/D");
+
+  // outgoing particles in lab frame (light/heavy)
+  double thetab, phib;
+  double Tb;
+  double thetaB, phiB, TB;
+  std::array<double, 2> T;
+  tree1->Branch("thetab", &thetab, "thetab/D"); // polar angle of light particle in lab frame
+  tree1->Branch("phib",     &phib, "phib/D"); // azimuthal angle of light particle in lab frame
+  tree1->Branch("Tb",         &Tb, "Tb/D"); // kinetic energy of light particle at vertex (before energy loss)
+  tree1->Branch("thetaB", &thetaB, "thetaB/D");
+  tree1->Branch("phiB",     &phiB, "phiB/D");
+  tree1->Branch("TB",         &TB, "TB/D"); // kinetic energy of heavy particle at vertex
+  tree1->Branch("T",          &T, "T/D");   // placeholder for true Q-value, currently set to 0 for simplicity
+
+  double thetab2, phib2;
+  double Tb2;
+  double thetaB2, phiB2, TB2;
+  std::array<double, 2> T2;
+  tree2->Branch("thetab", &thetab2, "thetab/D");
+  tree2->Branch("phib",     &phib2, "phib/D");
+  tree2->Branch("Tb",         &Tb2, "Tb/D");
+  tree2->Branch("thetaB", &thetaB2, "thetaB/D");
+  tree2->Branch("phiB",     &phiB2, "phiB/D");
+  tree2->Branch("TB",         &TB2, "TB/D");
+  tree2->Branch("T",          &T2, "T/D");
+
+  // excitation state identifiers
+  int ExAID;
+  double ExA;
+  tree1->Branch("ExAID", &ExAID, "ExAID/I"); // projectile excitation state ID
+  tree1->Branch("ExA",     &ExA, "ExA/D"); // projectile excitation energy in MeV
+
+  int ExAID2;
+  double ExA2;
+  tree2->Branch("ExAID", &ExAID2, "ExAID/I");
+  tree2->Branch("ExA",     &ExA2, "ExA/D");
+
+  int ExID;
+  double Ex;
+  tree1->Branch("ExID", &ExID, "ExID/I"); // target excitation state ID
+  tree1->Branch("Ex",     &Ex, "Ex/D"); // target excitation energy in MeV
+
+  int ExID2;
+  double Ex2;
+  tree2->Branch("ExID", &ExID2, "ExID/I");
+  tree2->Branch("Ex",     &Ex2, "Ex/D");
+
+  // true vertex position in target volume
+  double vertexX, vertexY, vertexZ;
+  tree1->Branch("vX",     &vertexX, "VertexX/D"); // true vertex X position in mm
+  tree1->Branch("vY",     &vertexY, "VertexY/D"); // true vertex Y position in mm
+  tree1->Branch("vZ",     &vertexZ, "VertexZ/D"); // true vertex Z position in mm
+
+  double vertexX2, vertexY2, vertexZ2;
+  tree2->Branch("vX",     &vertexX2, "VertexX/D");
+  tree2->Branch("vY",     &vertexY2, "VertexY/D");
+  tree2->Branch("vZ",     &vertexZ2, "VertexZ/D");
+
+  // reconstructed SX3 hit position
+  double sx3X, sx3Y, sx3Z;
+  tree1->Branch("sx3X",     &sx3X, "sx3X/D"); // reconstructed X position from SX3 (with optional smearing)
+  tree1->Branch("sx3Y",     &sx3Y, "sx3Y/D"); // reconstructed Y position from SX3 (with optional smearing)
+  tree1->Branch("sx3Z",     &sx3Z, "sx3Z/D"); // reconstructed Z position from SX3 (with optional smearing)
+
+  double sx3X2, sx3Y2, sx3Z2;
+  tree2->Branch("sx3X",     &sx3X2, "sx3X/D");
+  tree2->Branch("sx3Y",     &sx3Y2, "sx3Y/D");
+  tree2->Branch("sx3Z",     &sx3Z2, "sx3Z/D");
+
+  // PW nearest and next nearest wires
+  int anodeID[2], cathodeID[2];
+  int anodeID2[2], cathodeID2[2];
+  tree1->Branch("aID", anodeID, "anodeID/I"); // anodeID[0] is nearest anode wire, anodeID[1] is next nearest anode wire
+  tree1->Branch("cID", cathodeID, "cathodeID/I"); // cathodeID[0] is nearest cathode wire, cathodeID[1] is next nearest cathode wire
+  tree2->Branch("aID", anodeID2, "anodeID/I");
+  tree2->Branch("cID", cathodeID2, "cathodeID/I");
+
+  // distances to nearest wires
+  double anodeDist[2], cathodeDist[2];
+  double anodeDist2[2], cathodeDist2[2];
+  tree1->Branch("aDist",   anodeDist, "anodeDist/D");
+  tree1->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  tree2->Branch("aDist",   anodeDist2, "anodeDist/D");
+  tree2->Branch("cDist",  cathodeDist2, "cathodeDist/D");
+
+  // SX3 channel assignment and Z fraction (depth) information
+  int sx3ID, sx3Up, sx3Dn, sx3Bk;
+  double sx3ZFrac;
+  int sx3ID2, sx3Up2, sx3Dn2, sx3Bk2;
+  double sx3ZFrac2;
+  tree1->Branch("sx3ID",   &sx3ID, "sx3ID/I");
+  tree1->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  tree1->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree1->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree1->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  tree2->Branch("sx3ID",   &sx3ID2, "sx3ID/I");
+  tree2->Branch("sx3Up",   &sx3Up2, "sx3Up/I");
+  tree2->Branch("sx3Dn",   &sx3Dn2, "sx3Dn/I");
+  tree2->Branch("sx3Bk",   &sx3Bk2, "sx3Bk/I");
+  tree2->Branch("sx3ZFrac", &sx3ZFrac2, "sx3ZFrac/D");
+
+  // reconstructed angles from PW track fit, method 1 and 2
+  double reTheta, rePhi;
+  double reTheta2, rePhi2;
+  tree1->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  tree1->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  tree2->Branch("reTheta", &reTheta2, "reconstucted_theta/D");
+  tree2->Branch("rePhi",     &rePhi2, "reconstucted_phi/D");
+
+  double reTheta1, rePhi1;
+  double reTheta12, rePhi12;
+  tree1->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  tree1->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  tree2->Branch("reTheta1", &reTheta12, "reconstucted_theta1/D");
+  tree2->Branch("rePhi1",     &rePhi12, "reconstucted_phi1/D");
+
+  // reconstructed vertex Z from PW fit
+  double z0;
+  double z02;
+  tree1->Branch("z0",     &z0, "reconstucted_Z/D");
+  tree2->Branch("z0",     &z02, "reconstucted_Z/D");
+
+  //========timer
+  TBenchmark clock;
+  bool shown ;
+  clock.Reset();
+  clock.Start("timer");
+  shown = false;
+
+  //================================= Calculate event loop
+  for( int i = 0; i < numEvent ; i++){
+
+    // randomly sample target/projectile excitations
+    ExAID = gRandom->Integer(nExA);
+    ExA = ExAList[ExAID];
+    transfer.SetExA(ExA);
+
+    ExID = gRandom->Integer(nEx);
+    Ex = ExList[ExID];
+    transfer.SetExB(Ex);
+
+    // recalc kinematic constants for chosen states
+    transfer.CalReactionConstant();
+
+    // isotropic CM direction
+    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ;
+    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
+
+    //==== Calculate reaction kinematics in lab frame for the primary transfer
+    TLorentzVector * output = transfer.Event(thetaCM, phiCM); // returns array of outputs
+    TLorentzVector Pb = output[2]; // primary proton from transfer
+    TLorentzVector PB = output[3]; // excited 21Na* heavy product
+
+    thetab = Pb.Theta() * TMath::RadToDeg();
+    Tb = (Pb.E() - Pb.M()); // kinetic energy of the light proton from the primary transfer
+    thetaB = PB.Theta() * TMath::RadToDeg();
+    TB = (PB.E() - PB.M());
+    phib = Pb.Phi() * TMath::RadToDeg();
+    phiB = PB.Phi() * TMath::RadToDeg();
+    T[0] = Tb;
+    T[1] = TB;
+
+    // prepare secondary proton from 21Na* sequential decay
+    TLorentzVector decayProton;
+    TLorentzVector heavy20;
+    if(enableSequentialDecay){
+      heavy20 = SimulateSequentialDecay(PB, decayDaughterA, decayDaughterZ,
+                                       decayEjectA, decayEjectZ, decayProton);
+      thetab2 = decayProton.Theta() * TMath::RadToDeg();
+      phib2 = decayProton.Phi() * TMath::RadToDeg();
+      Tb2 = decayProton.E() - decayProton.M();
+      thetaB2 = heavy20.Theta() * TMath::RadToDeg();
+      phiB2 = heavy20.Phi() * TMath::RadToDeg();
+      TB2 = heavy20.E() - heavy20.M();
+      T2[0] = Tb2;
+      T2[1] = TB2;
+    } else {
+      thetab2 = TMath::QuietNaN();
+      phib2  = TMath::QuietNaN();
+      Tb2    = TMath::QuietNaN();
+      thetaB2 = TMath::QuietNaN();
+      phiB2 = TMath::QuietNaN();
+      TB2 = TMath::QuietNaN();
+      T2[0] = TMath::QuietNaN();
+      T2[1] = TMath::QuietNaN();
+    }
+
+    delete [] output;
+
+    // vertex position in target volume
+    vertexX = (vertexXRange[1]- vertexXRange[0])*gRandom->Rndm() +  vertexXRange[0];
+    vertexY = (vertexYRange[1]- vertexYRange[0])*gRandom->Rndm() +  vertexYRange[0];
+    vertexZ = (vertexZRange[1]- vertexZRange[0])*gRandom->Rndm() +  vertexZRange[0];
+
+    TVector3 vertex(vertexX, vertexY, vertexZ);
+
+    // set direction vector from lab angle
+    TVector3 dir(1, 0, 0);
+    dir.SetTheta(thetab * TMath::DegToRad());
+    dir.SetPhi(phib * TMath::DegToRad());
+
+    // run detector response models for PW and SX3
+    pw->FindWireID(vertex, dir, false);
+    sx3->FindSX3Pos(vertex, dir, false);
+
+    PWHitInfo hitInfo = pw->GetHitInfo();
+
+    anodeID[0]   = hitInfo.nearestWire.first; // nearest anode wire ID
+    cathodeID[0] = hitInfo.nearestWire.second; // nearest cathode wire ID
+    anodeID[1]   = hitInfo.nextNearestWire.first; // next nearest anode wire ID
+    cathodeID[1] = hitInfo.nextNearestWire.second; // next nearest cathode wire ID
+
+    anodeDist[1]   = hitInfo.nextNearestDist.first; // distance to next nearest anode wire
+    cathodeDist[1] = hitInfo.nextNearestDist.second; // distance to next nearest cathode wire
+
+    if(IsDeadAnode(anodeID[0])) continue;
+    if(IsDeadCathode(cathodeID[0])) continue;
+
+    // SX3 hit channel info and depth fraction
+    sx3ID = sx3->GetID();
+
+    if(IsDeadSX3(sx3ID)) continue;
+
+    anodeDist[0]   = hitInfo.nearestDist.first; // distance to nearest anode wire
+    cathodeDist[0] = hitInfo.nearestDist.second; // distance to nearest cathode wire
+
+    if( sx3ID >= 0 ){
+      sx3Up    = sx3->GetChUp();
+      sx3Dn    = sx3->GetChDn();
+      sx3Bk    = sx3->GetChBk();
+      sx3ZFrac = sx3->GetZFrac();
+      
+      // apply intrinsic detector resolution to true SX3 hit position
+      // for no smearing comment out and use GetHitPos();
+      TVector3 hitPos = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+
+      sx3X = hitPos.X();
+      sx3Y = hitPos.Y();
+      sx3Z = hitPos.Z();
+
+      // store track data for visualization if enabled
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+      // reconstruct track from PW readings + SX3 hit
+      pw->CalTrack(hitPos, anodeID[0], cathodeID[0], false);
+      reTheta = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      // alternative track algorithm with uncertainty parameters
+      pw->CalTrack2(hitPos, hitInfo, sigmaPW_A, sigmaPW_C, false);
+      reTheta1 = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi1   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      z0 = pw->GetZ0();
+      tree1->Fill();
+
+      // fill tree2 using the secondary proton (proton 2) track
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      pw->FindWireID(vertex, dir2, false);
+      sx3->FindSX3Pos(vertex, dir2, false);
+      PWHitInfo hitInfo2 = pw->GetHitInfo();
+
+      anodeID2[0]   = hitInfo2.nearestWire.first;
+      cathodeID2[0] = hitInfo2.nearestWire.second;
+      anodeID2[1]   = hitInfo2.nextNearestWire.first;
+      cathodeID2[1] = hitInfo2.nextNearestWire.second;
+
+      anodeDist2[1]   = hitInfo2.nextNearestDist.first;
+      cathodeDist2[1] = hitInfo2.nextNearestDist.second;
+
+      if(IsDeadAnode(anodeID2[0]) || IsDeadCathode(cathodeID2[0])){
+        sx3ID2 = -1;
+      } else {
+        sx3ID2 = sx3->GetID();
+      }
+
+      if(sx3ID2 < 0 || IsDeadSX3(sx3ID2)){
+        sx3ID2 = -1;
+        sx3Up2 = -1;
+        sx3Dn2 = -1;
+        sx3Bk2 = -1;
+        sx3ZFrac2 = TMath::QuietNaN();
+        sx3X2 = TMath::QuietNaN();
+        sx3Y2 = TMath::QuietNaN();
+        sx3Z2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+      } else {
+        anodeDist2[0]   = hitInfo2.nearestDist.first;
+        cathodeDist2[0] = hitInfo2.nearestDist.second;
+        sx3Up2    = sx3->GetChUp();
+        sx3Dn2    = sx3->GetChDn();
+        sx3Bk2    = sx3->GetChBk();
+        sx3ZFrac2 = sx3->GetZFrac();
+        TVector3 hitPos2 = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+        sx3X2 = hitPos2.X();
+        sx3Y2 = hitPos2.Y();
+        sx3Z2 = hitPos2.Z();
+        pw->CalTrack(hitPos2, anodeID2[0], cathodeID2[0], false);
+        reTheta2 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi2   = pw->GetTrackPhi() * TMath::RadToDeg();
+        pw->CalTrack2(hitPos2, hitInfo2, sigmaPW_A, sigmaPW_C, false);
+        reTheta12 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi12   = pw->GetTrackPhi() * TMath::RadToDeg();
+        z02       = pw->GetZ0();
+      }
+
+      // copy common event info to tree2
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+
+      tree2->Fill();
+
+    }else{
+      // no valid SX3 hit: mark clearly invalid
+      sx3Up = -1;
+      sx3Dn = -1;
+      sx3Bk = -1;
+      sx3ZFrac = TMath::QuietNaN();
+
+      sx3X = TMath::QuietNaN();
+      sx3Y = TMath::QuietNaN();
+      sx3Z = TMath::QuietNaN();
+
+      reTheta  = TMath::QuietNaN();
+      rePhi    = TMath::QuietNaN();
+      reTheta1 = TMath::QuietNaN();
+      rePhi1   = TMath::QuietNaN();
+      z0       = TMath::QuietNaN();
+      //Tb = -12354567; // mark kinetic energy as invalid for no hit case
+      // fill tree with original data (no energy loss for these events)
+      //comment out tree fill for no hit case  
+      //tree->Fill();
+    }
+
+    //#################################################################### Timer
+    // measure elapsed real time and print progress roughly every 10 sec
+    clock.Stop("timer");
+    Double_t time = clock.GetRealTime("timer");
+    clock.Start("timer");
+
+    if ( !shown ) {
+      if (fmod(time, 10) < 1 ){
+        printf( "%10d[%2d%%]| %8.2f sec | expect: %5.1f min \n", i, TMath::Nint((i+1)*100./numEvent), time , numEvent*time/(i+1)/60);
+        shown = 1;
+      }
+    } else {
+      if (fmod(time, 10) > 9 ){
+        shown = 0;
+      }
+    }
+
+  }
+
+  // write results to ROOT file and close
+  tree1->Write("", TObject::kOverwrite);
+  tree2->Write("", TObject::kOverwrite);
+  int count1 = tree1->GetEntries();
+  int count2 = tree2->GetEntries();
+  saveFile->Close();
+
+  printf("=============== done. saved as %s. tree1 entries: %d, tree2 entries: %d\n", saveFileName.Data(), count1, count2);
+
+  if(enableVis){ // to enable visualization, run with 3rd argument "vis", e.g. "./anasenMC 1000 vis"
+    printf("Displaying geometry with %zu tracks from simulation\n", visTrackVertex.size());
+    
+    // Build full geometry with all wires
+    anasen->DrawAnasen(0, 23, 0, 23, -1, true);
+    
+    // Add all stored tracks to the geometry
+    TGeoManager *geom = anasen->GetGeoManager();
+    TGeoVolume *worldBox = anasen->GetWorldBox();
+    
+    if(geom && worldBox && visTrackVertex.size() > 0){
+      int trackNodeID = 500;  // start node IDs for tracks
+      
+      for(size_t iTrack = 0; iTrack < visTrackVertex.size(); ++iTrack){
+        TVector3 vertex = visTrackVertex[iTrack];
+        TVector3 dir = visTrackDir[iTrack];
+        TVector3 hitPos = visTrackHitPos[iTrack];
+        
+        double theta = dir.Theta() * TMath::RadToDeg();
+        double phi = dir.Phi() * TMath::RadToDeg();
+        
+        // Add a line marker at the vertex
+        TGeoVolume *startMarker = geom->MakeSphere("startMarker", 0, 0, 2.0);
+        startMarker->SetLineColor(kBlack);
+        worldBox->AddNode(startMarker, trackNodeID, 
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(), 
+                                          new TGeoRotation("rot", 0, 0, 0)));
+        trackNodeID++;
+        
+        // Add track line from vertex toward hit position
+        TGeoVolume *trackLine = geom->MakeTube("trackLine", 0, 0, 0.08, 150.0);
+        trackLine->SetLineColor(kBlue);
+        worldBox->AddNode(trackLine, trackNodeID,
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(),
+                                          new TGeoRotation("rotTrack", phi + 90, theta, 0)));
+        trackNodeID++;
+        
+        // Add hit position marker
+        TGeoVolume *hitMarker = geom->MakeSphere("hitMarker", 0, 0, 2.0);
+        hitMarker->SetLineColor(kRed);
+        worldBox->AddNode(hitMarker, trackNodeID,
+                         new TGeoCombiTrans(hitPos.X(), hitPos.Y(), hitPos.Z(),
+                                          new TGeoRotation("rotHit", 0, 0, 0)));
+        trackNodeID++;
+      }
+      
+      // Redraw geometry with all tracks
+      geom->CloseGeometry();
+      geom->SetVisLevel(4);
+      worldBox->Draw("ogle");
+    }
+    
+    if(app){
+      printf("Entering ROOT event loop\n");
+      app->Run();
+    }
+  }
+
+  delete anasen;
+
+
+  return 0;
+
+}

Armory/anasenMS.cpp

@@ -1,18 +1,90 @@
-#include "TRandom.h"
-#include "TFile.h"
-#include "TTree.h"
-#include "TH1.h"
-#include "TH2.h"
-#include "TStyle.h"
-#include "TCanvas.h"
-#include "TBenchmark.h"
+#include "TRandom.h"      // ROOT random number generators, gRandom
+#include "TFile.h"        // ROOT file I/O
+#include "TTree.h"        // ROOT tree storage
+#include "TH1.h"          // 1D histograms
+#include "TH2.h"          // 2D histograms
+#include "TStyle.h"       // ROOT plotting style controls
+#include "TCanvas.h"      // ROOT canvas drawing
+#include "TBenchmark.h"   // timing measurement
+#include "TGraph.h"       // for energy loss interpolation
+#include <cstring>
+#include "TApplication.h" // ROOT app loop
+#include "ClassTransfer.h" // Reaction kinematics and MC event generation
+#include "ClassAnasen.h"   // ANASEN detector model classes (SX3, PW, etc.)
+#include "ClassQQQ.h"      // QQQ detector model class
+#include <stdio.h>
+#include <stdlib.h>
+#include <set>
+#include "TLegend.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
 
-#include "ClassTransfer.h"
-#include "ClassAnasen.h"
+//======== Generate light particle based on reaction
+// calculate real and reconstructed tracks and Q-value uncertainty
 
-//======== Gerneate light particle based on reaction
-// find out the CalTrack and the real track
-// find out the Q-value uncertaintly
+// Function to load energy loss table from file
+TGraph* LoadELoss(const char* filename) {
+  TGraph* g = new TGraph(filename, "%lg %lg");
+  return g;
+}
+
+bool IsDeadAnode(int id){
+    static std::set<int> dead = {}; // add dead anode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadCathode(int id){
+    static std::set<int> dead = {}; // add dead cathode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadSX3(int id){ 
+    static std::set<int> dead = {}; // add dead SX3 IDs here, 0-23 1,7,9,3
+    return dead.count(id);
+}
+
+// Simulate sequential two-body decay of an unstable parent in its rest frame.
+TLorentzVector SimulateSequentialDecay(const TLorentzVector &parent,
+                                       int daughterA, int daughterZ,
+                                       int ejectA, int ejectZ,
+                                       TLorentzVector &ejectileOut){
+  Isotope daughter(daughterA, daughterZ);
+  Isotope ejectile(ejectA, ejectZ);
+
+  double M = parent.M();
+  double mD = daughter.Mass;
+  double mE = ejectile.Mass;
+
+  double sqM = M * M;
+  double sum = mD + mE;
+  double diff = mD - mE;
+  double p2 = (sqM - sum*sum) * (sqM - diff*diff) / (4.0 * sqM); // two-body decay momentum squared
+  if( p2 < 0 ) p2 = 0; // handle unphysical case where parent mass is less than sum of daughter and ejectile masses
+  double p = TMath::Sqrt(p2); // two-body decay momentum
+
+  double cosTheta = 2.0 * gRandom->Rndm() - 1.0; // isotropic decay in parent rest frame
+  double theta = TMath::ACos(cosTheta); // polar angle of daughter in parent rest frame
+  double phi = gRandom->Rndm() * TMath::TwoPi(); // azimuthal angle of daughter in parent rest frame
+
+  TVector3 v; // momentum vector of daughter in parent rest frame
+  v.SetMagThetaPhi(p, theta, phi); // daughter momentum in parent rest frame
+
+  TLorentzVector daughterLab; // daughter 4-vector in lab frame, initialized with momentum from decay and mass of daughter
+  daughterLab.SetVectM(v, mD); // set daughter 4-vector in parent rest frame, then boost to lab frame
+
+  TLorentzVector ejectileLab; // ejectile 4-vector in lab frame, initialized with momentum opposite to daughter and mass of ejectile
+  ejectileLab.SetVectM(-v, mE); //  set ejectile 4-vector in parent rest frame, then boost to lab frame
+
+  TVector3 boost = parent.BoostVector(); // boost vector to go from parent rest frame to lab frame
+  daughterLab.Boost(boost); // boost daughter to lab frame
+  ejectileLab.Boost(boost); // boost ejectile to lab frame
+
+  ejectileOut = ejectileLab; // return ejectile in lab frame
+  return daughterLab;
+}
 
 int main(int argc, char **argv){
 
@@ -20,33 +92,49 @@ int main(int argc, char **argv){
   printf("===       ANASEN Monte Carlo          ===\n");
   printf("=========================================\n");
 
+  // number of events can be overridden from command line
   int numEvent = 1000000;
   if( argc >= 2 ) numEvent = atoi(argv[1]);
-
-  //Reaction
   TransferReaction transfer;
 
-  transfer.SetA(24,12, 0);
-  transfer.SetIncidentEnergyAngle(10, 0, 0);
-  transfer.Seta( 4, 2);
-  transfer.Setb( 1, 1);
+  //To set beam energy loss, use energy loss app, and create table with target isotope, set Initial beam energy as max energy 
+  transfer.SetA(18, 9, 0);            // 18Ne projectile
+  //TGraph* elossBeam = LoadELoss("../ELoss/HeLoss/E_vs_x_Na-21.dat");
+  transfer.Seta(4, 2);                 // 4He target
+  transfer.Setb(1, 1);                 // outgoing proton from the primary transfer
+  transfer.SetB(21, 11);               // 21Na* heavy product
+  const ReactionConfig reactionConfig = transfer.GetRectionConfig();
+  const double beamA = reactionConfig.beamA;                   // mass number of 14N beam
+  const double beamE = 3;                // maximum beam energy in MeV/u
 
-  //TODO add alpha source
+  const int kMBeam = reactionConfig.beamA; // mass number of beam
+  const int kMTarget = reactionConfig.targetA; // mass number of target
+  const int kMLight = reactionConfig.recoilLightA; // mass number of light ejectile
+  const int kMHeavy = reactionConfig.recoilHeavyA; // mass number of heavy product
+  bool enableSequentialDecay = false; // turning to false to disable sequential decay for now, can be set to true to enable
+  const int decayDaughterA = 20;
+  const int decayDaughterZ = 10;
+  const int decayEjectA = 1;
+  const int decayEjectZ = 1;
 
-  std::vector<float> ExAList = {0};
-  std::vector<float> ExList = {0, 1, 2};
+  // Excited state lists (projectile and heavy-product excitation states)
+  std::vector<float> ExAList = {0};              // Beam excited energy
+  std::vector<float> ExList = {0, .3, 1.7, 2.4, 2.8, 3.5, 3.9, 4, 4.3, 4.5};             // Heavy product excited energy
 
-  double vertexXRange[2] = {   -5,    5}; // mm
-  double vertexYRange[2] = {   -5,    5}; 
-  double vertexZRange[2] = { -100,  100}; 
+  // define vertex position uniform distribution ranges (mm)
+  double vertexXRange[2] = {   -5, 5}; // mm - 5, 5
+  double vertexYRange[2] = {   -5, 5}; // -5, 5
+  double vertexZRange[2] = { -174.3, 174.3}; // -174.3, 174.3 (full length of gas volume, centered at 0)
+  const double beamEntranceZ = -280; //vertexZRange[0]; // mm, assumed beam entrance into the gas
 
-  double sigmaSX3_W = -1; // mm, < 0 use mid-point
-  double sigmaSX3_L = 3; // mm, < 0 use mid-point
-  double sigmaPW_A  = 0; // from 0 to 1.
-  double sigmaPW_C  = 0; // from 0 to 1.
 
-  //###################################################
+  // detector resolution / uncertainty parameters
+  double sigmaSX3_W = 0; // mm, if < 0 use mid-point (no spread in SX3 horizontal dimension)
+  double sigmaSX3_L = 0;  // mm, vertical spread for SX3
+  double sigmaPW_A  = 0;  // normalized anode uncertainty term (0-1)
+  double sigmaPW_C  = 0;  // normalized cathode uncertainty term (0-1)
 
+  // status printout
   printf("------------ Vertex :\n");
   printf("X : %7.2f - %7.2f mm\n", vertexXRange[0], vertexXRange[1]);
   printf("Y : %7.2f - %7.2f mm\n", vertexYRange[0], vertexYRange[1]);
@@ -57,83 +145,216 @@ int main(int argc, char **argv){
   printf("          Anode : %.1f mm\n", sigmaPW_A);
   printf("        Cathode : %.1f mm\n", sigmaPW_C);
   printf("        num_eve : %d \n",numEvent);
+
+  // calculates energy/momentum/kinematics constants for transfer reaction
   transfer.CalReactionConstant();
 
   int nExA = ExAList.size();
   int nEx  = ExList.size();
 
-  ANASEN * anasen = new ANASEN();
-  SX3 * sx3 = anasen->GetSX3();    
-  PW * pw = anasen->GetPW(); 
+  // optional visualization control: pass "vis" as 3rd arg
+  bool enableVis = (argc >= 3 && strcmp(argv[2], "vis") == 0);
+  TApplication *app = nullptr;
+  if(enableVis){
+    app = new TApplication("anasenVis", &argc, argv);
+  }
 
+  // storage for tracks during simulation (for visualization)
+  std::vector<TVector3> visTrackVertex, visTrackDir, visTrackHitPos;
+  std::vector<std::pair<int,int>> visTrackWires;  // {anodeID, cathodeID}
+
+  // create detector representation in memory
+  ANASEN * anasen = new ANASEN();       // top-level detector object
+  SX3 * sx3 = anasen->GetSX3();         // silicon array part
+  PW * pw = anasen->GetPW();            // proportional wire chamber part
+  QQQ * qqq = anasen->GetQQQ();         // optional QQQ detector part, not used in this simulation but can be enabled for visualization
+
+  // output file + trees
   TString saveFileName = "SimAnasen1.root";
   printf("\e[32m#################################### building Tree in %s\e[0m\n", saveFileName.Data());
   TFile * saveFile = new TFile(saveFileName, "recreate");
-  TTree * tree = new TTree("tree", "tree");
+  //TFile * saveFile2 = new TFile("SimAnasen2.root", "recreate");
+  TTree * tree1 = new TTree("tree1", "tree1");
+  TTree * tree2 = new TTree("tree2", "tree2");
+  //TTree * tree3 = new TTree("tree3", "tree3"); // only includes Tb and thetab
 
+  // beam and CM variables saved in tree
   double KEA;
-  tree->Branch("beamKEA",     &KEA, "beamKEA/D");
+  double KEA2;
+  double beamPath_cm;
+  double beamEnergy;
+  double beamEnergyLoss;
+  int MBeamOut;
+  int MTargetOut;
+  int MLightOut;
+  int MHeavyOut;
+  tree1->Branch("beamKEA",      &KEA, "beamKEA/D");
+  tree2->Branch("beamKEA",      &KEA2, "beamKEA/D");
+  tree1->Branch("beamPath_cm",  &beamPath_cm, "beamPath_cm/D");
+  tree2->Branch("beamPath_cm",  &beamPath_cm, "beamPath_cm/D");
+  tree1->Branch("beamEnergy",   &beamEnergy, "beamEnergy/D");
+  tree2->Branch("beamEnergy",   &beamEnergy, "beamEnergy/D");
+  tree1->Branch("beamEnergyLoss", &beamEnergyLoss, "beamEnergyLoss/D");
+  tree2->Branch("beamEnergyLoss", &beamEnergyLoss, "beamEnergyLoss/D");
+  tree1->Branch("MBeam", &MBeamOut, "MBeam/I");
+  tree1->Branch("MTarget", &MTargetOut, "MTarget/I");
+  tree1->Branch("MLight", &MLightOut, "MLight/I");
+  tree1->Branch("MHeavy", &MHeavyOut, "MHeavy/I");
+  tree2->Branch("MBeam", &MBeamOut, "MBeam/I");
+  tree2->Branch("MTarget", &MTargetOut, "MTarget/I");
+  tree2->Branch("MLight", &MLightOut, "MLight/I");
+  tree2->Branch("MHeavy", &MHeavyOut, "MHeavy/I");
+
+  // constant reaction mass numbers stored in every event entry
+  MBeamOut = kMBeam;
+  MTargetOut = kMTarget;
+  MLightOut = kMLight;
+  MHeavyOut = kMHeavy;
 
   double thetaCM, phiCM;
-  tree->Branch("thetaCM", &thetaCM, "thetaCM/D");
-  tree->Branch("phiCM",     &phiCM, "phiCM/D");
+  double thetaCM2, phiCM2;
+  tree1->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  tree1->Branch("phiCM",     &phiCM, "phiCM/D");
+  tree2->Branch("thetaCM", &thetaCM2, "thetaCM/D");
+  tree2->Branch("phiCM",     &phiCM2, "phiCM/D");
 
-  double thetab, phib, Tb;
-  double thetaB, phiB, TB;
-  tree->Branch("thetab", &thetab, "thetab/D");
-  tree->Branch("phib",     &phib, "phib/D");
-  tree->Branch("Tb",         &Tb, "Tb/D");
-  tree->Branch("thetaB", &thetaB, "thetaB/D");
-  tree->Branch("phiB",     &phiB, "phiB/D");
-  tree->Branch("TB",         &TB, "TB/D");
+  // outgoing particles in lab frame (light/heavy)
+  double thetab, phib, Tb, qqqTb;
+  double thetaB, phiB, TB, qqqTB;
+  std::array<double, 2> T;
+  tree1->Branch("thetab", &thetab, "thetab/D"); // polar angle of light particle in lab frame
+  tree1->Branch("phib",     &phib, "phib/D"); // azimuthal angle of light particle in lab frame
+  tree1->Branch("Tb",         &Tb, "Tb/D"); // kinetic energy of light particle at vertex (before energy loss)
+  tree1->Branch("thetaB", &thetaB, "thetaB/D");
+  tree1->Branch("phiB",     &phiB, "phiB/D");
+  tree1->Branch("TB",         &TB, "TB/D"); // kinetic energy of heavy particle at vertex (before energy loss)
+  tree1->Branch("T",          &T, "T/D");   // placeholder for true Q-value, currently set to 0 for simplicity
+  tree1->Branch("qqqTb", &qqqTb, "qqqTb/D"); // kinetic energy of light particle at vertex (before energy loss) for events where the light particle hits the QQQ, currently set to 0 for simplicity
+  tree1->Branch("qqqTB", &qqqTB, "qqqTB/D"); // kinetic energy of heavy particle at vertex (before energy loss) for events where the light
 
+  double thetab2, phib2, Tb2, qqqTb2;
+  double thetaB2, phiB2, TB2, qqqTB2;
+  std::array<double, 2> T2;
+  tree2->Branch("thetab", &thetab2, "thetab/D");
+  tree2->Branch("phib",     &phib2, "phib/D");
+  tree2->Branch("Tb",         &Tb2, "Tb/D");
+  tree2->Branch("thetaB", &thetaB2, "thetaB/D");
+  tree2->Branch("phiB",     &phiB2, "phiB/D");
+  tree2->Branch("TB",         &TB2, "TB/D");
+  tree2->Branch("T",          &T2, "T/D");
+  tree2->Branch("qqqTb", &qqqTb2, "qqqTb/D");
+  tree2->Branch("qqqTB", &qqqTB2, "qqqTB/D");
+
+  //tree3->Branch("Tb", &Tb, "Tb/D");
+  //tree3->Branch("thetab", &thetab, "thetab/D");
+
+  // excitation state identifiers
   int ExAID;
   double ExA;
-  tree->Branch("ExAID", &ExAID, "ExAID/I");
-  tree->Branch("ExA",     &ExA, "ExA/D");
+  tree1->Branch("ExAID", &ExAID, "ExAID/I"); // projectile excitation state ID
+  tree1->Branch("ExA",     &ExA, "ExA/D"); // projectile excitation energy in MeV
+
+  int ExAID2;
+  double ExA2;
+  tree2->Branch("ExAID", &ExAID2, "ExAID/I");
+  tree2->Branch("ExA",     &ExA2, "ExA/D");
 
   int ExID;
   double Ex;
-  tree->Branch("ExID", &ExID, "ExID/I");
-  tree->Branch("Ex",     &Ex, "Ex/D");
+  tree1->Branch("ExID", &ExID, "ExID/I"); // target excitation state ID
+  tree1->Branch("Ex",     &Ex, "Ex/D"); // target excitation energy in MeV
 
+  int ExID2;
+  double Ex2;
+  tree2->Branch("ExID", &ExID2, "ExID/I");
+  tree2->Branch("Ex",     &Ex2, "Ex/D");
+
+  // true vertex position in target volume
   double vertexX, vertexY, vertexZ;
-  tree->Branch("vX",     &vertexX, "VertexX/D");
-  tree->Branch("vY",     &vertexY, "VertexY/D");
-  tree->Branch("vZ",     &vertexZ, "VertexZ/D");
+  tree1->Branch("vX",     &vertexX, "VertexX/D"); // true vertex X position in mm
+  tree1->Branch("vY",     &vertexY, "VertexY/D"); // true vertex Y position in mm
+  tree1->Branch("vZ",     &vertexZ, "VertexZ/D"); // true vertex Z position in mm
 
+  double vertexX2, vertexY2, vertexZ2;
+  tree2->Branch("vX",     &vertexX2, "VertexX/D");
+  tree2->Branch("vY",     &vertexY2, "VertexY/D");
+  tree2->Branch("vZ",     &vertexZ2, "VertexZ/D");
+
+  // reconstructed SX3 hit position
   double sx3X, sx3Y, sx3Z;
-  tree->Branch("sx3X",     &sx3X, "sx3X/D");
-  tree->Branch("sx3Y",     &sx3Y, "sx3Y/D");
-  tree->Branch("sx3Z",     &sx3Z, "sx3Z/D");
+  tree1->Branch("sx3X",     &sx3X, "sx3X/D"); // reconstructed X position from SX3 (with optional smearing) in mm
+  tree1->Branch("sx3Y",     &sx3Y, "sx3Y/D"); // reconstructed Y position from SX3 (with optional smearing)
+  tree1->Branch("sx3Z",     &sx3Z, "sx3Z/D"); // reconstructed Z position from SX3 (with optional smearing)
 
+  double sx3X2, sx3Y2, sx3Z2;
+  tree2->Branch("sx3X",     &sx3X2, "sx3X/D");
+  tree2->Branch("sx3Y",     &sx3Y2, "sx3Y/D");
+  tree2->Branch("sx3Z",     &sx3Z2, "sx3Z/D");
+
+  double qqqX, qqqY, qqqZ;
+  tree1->Branch("qqqX",     &qqqX, "qqqX/D"); // reconstructed X position from QQQ (with optional smearing) in mm
+  tree1->Branch("qqqY",     &qqqY, "qqqY/D"); // reconstructed Y position from QQQ (with optional smearing)
+  tree1->Branch("qqqZ",     &qqqZ, "qqqZ/D"); // reconstructed Z position from QQQ (with optional smearing)
+
+  double qqqX2, qqqY2, qqqZ2;
+  tree2->Branch("qqqX",     &qqqX2, "qqqX/D");
+  tree2->Branch("qqqY",     &qqqY2, "qqqY/D");
+  tree2->Branch("qqqZ",     &qqqZ2, "qqqZ/D");
+
+  // PW nearest and next nearest wires
   int anodeID[2], cathodeID[2];
-  tree->Branch("aID", anodeID, "anodeID/I");
-  tree->Branch("cID", cathodeID, "cathodeID/I");
+  int anodeID2[2], cathodeID2[2];
+  tree1->Branch("aID", anodeID, "anodeID/I"); // anodeID[0] is nearest anode wire, anodeID[1] is next nearest anode wire
+  tree1->Branch("cID", cathodeID, "cathodeID/I"); // cathodeID[0] is nearest cathode wire, cathodeID[1] is next nearest cathode wire
+  tree2->Branch("aID", anodeID2, "anodeID/I");
+  tree2->Branch("cID", cathodeID2, "cathodeID/I");
 
+  // distances to nearest wires
   double anodeDist[2], cathodeDist[2];
-  tree->Branch("aDist",   anodeDist, "anodeDist/D");
-  tree->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  double anodeDist2[2], cathodeDist2[2];
+  tree1->Branch("aDist",   anodeDist, "anodeDist/D");
+  tree1->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  tree2->Branch("aDist",   anodeDist2, "anodeDist/D");
+  tree2->Branch("cDist",  cathodeDist2, "cathodeDist/D");
 
-  int sx3ID, sx3Up, sx3Dn, sx3Bk;
+  // SX3 channel assignment and Z fraction (depth) information
+  int sx3ID, sx3Up, sx3Dn, sx3Bk, qqqID;
   double sx3ZFrac;
-  tree->Branch("sx3ID",   &sx3ID, "sx3ID/I");
-  tree->Branch("sx3Up",   &sx3Up, "sx3Up/I");
-  tree->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
-  tree->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
-  tree->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  int sx3ID2, sx3Up2, sx3Dn2, sx3Bk2, qqqID2;
+  double sx3ZFrac2;
+  tree1->Branch("sx3ID",   &sx3ID, "sx3ID/I");
+  tree1->Branch("qqqID",   &qqqID, "qqqID/I");
+  tree1->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  tree1->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree1->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree1->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  tree2->Branch("sx3ID",   &sx3ID2, "sx3ID/I");
+  tree2->Branch("qqqID",   &qqqID2, "qqqID/I");
+  tree2->Branch("sx3Up",   &sx3Up2, "sx3Up/I");
+  tree2->Branch("sx3Dn",   &sx3Dn2, "sx3Dn/I");
+  tree2->Branch("sx3Bk",   &sx3Bk2, "sx3Bk/I");
+  tree2->Branch("sx3ZFrac", &sx3ZFrac2, "sx3ZFrac/D");
 
+  // reconstructed angles from PW track fit, method 1 and 2
   double reTheta, rePhi;
-  tree->Branch("reTheta", &reTheta, "reconstucted_theta/D");
-  tree->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  double reTheta2, rePhi2;
+  tree1->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  tree1->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  tree2->Branch("reTheta", &reTheta2, "reconstucted_theta/D");
+  tree2->Branch("rePhi",     &rePhi2, "reconstucted_phi/D");
 
   double reTheta1, rePhi1;
-  tree->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
-  tree->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  double reTheta12, rePhi12;
+  tree1->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  tree1->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  tree2->Branch("reTheta1", &reTheta12, "reconstucted_theta1/D");
+  tree2->Branch("rePhi1",     &rePhi12, "reconstucted_phi1/D");
 
+  // reconstructed vertex Z from PW fit
   double z0;
-  tree->Branch("z0",     &z0, "reconstucted_Z/D");
-
+  double z02;
+  tree1->Branch("z0",     &z0, "reconstucted_Z/D");
+  tree2->Branch("z0",     &z02, "reconstucted_Z/D");
 
   //========timer
   TBenchmark clock;
@@ -142,9 +363,10 @@ int main(int argc, char **argv){
   clock.Start("timer");
   shown = false;
 
-  //================================= Calculate event
+  //================================= Calculate event loop
   for( int i = 0; i < numEvent ; i++){
 
+    // randomly sample target/projectile excitations
     ExAID = gRandom->Integer(nExA);
     ExA = ExAList[ExAID];
     transfer.SetExA(ExA);
@@ -153,77 +375,218 @@ int main(int argc, char **argv){
     Ex = ExList[ExID];
     transfer.SetExB(Ex);
 
+    // recalc kinematic constants for chosen states
     transfer.CalReactionConstant();
 
-    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ; 
-    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
-
-    //==== Calculate reaction
-    TLorentzVector * output = transfer.Event(thetaCM, phiCM);
-    TLorentzVector Pb = output[2];
-    TLorentzVector PB = output[3];
-
-    thetab = Pb.Theta() * TMath::RadToDeg();
-    thetaB = PB.Theta() * TMath::RadToDeg();
-
-    Tb = Pb.E() - Pb.M();
-    TB = PB.E() - PB.M();
-
-    phib = Pb.Phi() * TMath::RadToDeg();
-    phiB = PB.Phi() * TMath::RadToDeg();
-
+    // vertex position in target volume
     vertexX = (vertexXRange[1]- vertexXRange[0])*gRandom->Rndm() +  vertexXRange[0];
     vertexY = (vertexYRange[1]- vertexYRange[0])*gRandom->Rndm() +  vertexYRange[0];
     vertexZ = (vertexZRange[1]- vertexZRange[0])*gRandom->Rndm() +  vertexZRange[0];
 
     TVector3 vertex(vertexX, vertexY, vertexZ);
 
+    // compute beam energy at the event vertex from the gas path length
+    beamPath_cm = TVector3(vertexZ - beamEntranceZ, vertexX, vertexY).Mag() * 0.1;
+    if( beamPath_cm < 0 ) beamPath_cm = 0;
+    //beamEnergy = elossBeam->Eval(beamPath_cm); // MeV
+    //beamEnergyLoss = elossBeam->Eval(0.0) - beamEnergy;
+    //KEA = beamEnergy / beamA;
+    KEA = gRandom->Uniform(0, beamE);
+    beamEnergy = KEA * beamA;
+    beamEnergyLoss = 0;
+    transfer.SetIncidentEnergyAngle(KEA, 0, 0);
+    transfer.CalReactionConstant();
+
+    // isotropic CM direction
+    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ; // polar angle in CM frame
+    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
+
+    //==== Calculate reaction kinematics in lab frame for the primary transfer
+    TLorentzVector * output = transfer.Event(thetaCM, phiCM); // returns array of outputs
+    TLorentzVector Pb = output[2]; // primary proton from transfer
+    TLorentzVector PB = output[3]; // excited 21Na* heavy product
+
+    thetab = Pb.Theta() * TMath::RadToDeg();
+    Tb = (Pb.E() - Pb.M()); // kinetic energy of the light proton from the primary transfer
+    thetaB = PB.Theta() * TMath::RadToDeg();
+    TB = (PB.E() - PB.M());
+    phib = Pb.Phi() * TMath::RadToDeg();
+    phiB = PB.Phi() * TMath::RadToDeg();
+    T[0] = Tb;
+    T[1] = TB;
+
+    //secondary decay
+    TLorentzVector decayProton;
+    TLorentzVector heavy20;
+    if(enableSequentialDecay){
+      heavy20 = SimulateSequentialDecay(PB, decayDaughterA, decayDaughterZ,
+                                       decayEjectA, decayEjectZ, decayProton);
+      thetab2 = decayProton.Theta() * TMath::RadToDeg();
+      phib2 = decayProton.Phi() * TMath::RadToDeg();
+      Tb2 = decayProton.E() - decayProton.M();
+      thetaB2 = heavy20.Theta() * TMath::RadToDeg();
+      phiB2 = heavy20.Phi() * TMath::RadToDeg();
+      TB2 = heavy20.E() - heavy20.M();
+      T2[0] = Tb2;
+      T2[1] = TB2;
+    } else {
+      thetab2 = TMath::QuietNaN();
+      phib2  = TMath::QuietNaN();
+      Tb2    = TMath::QuietNaN();
+      thetaB2 = TMath::QuietNaN();
+      phiB2 = TMath::QuietNaN();
+      TB2 = TMath::QuietNaN();
+      T2[0] = TMath::QuietNaN();
+      T2[1] = TMath::QuietNaN();
+    }
+
+    delete [] output;
+
+    // set direction vector from lab angle
     TVector3 dir(1, 0, 0);
     dir.SetTheta(thetab * TMath::DegToRad());
     dir.SetPhi(phib * TMath::DegToRad());
 
-   
+    // run detector response models for PW and SX3
     pw->FindWireID(vertex, dir, false);
     sx3->FindSX3Pos(vertex, dir, false);
+    qqq->FindQQQPos(vertex, dir, false);
 
     PWHitInfo hitInfo = pw->GetHitInfo();
 
-    anodeID[0]   = hitInfo.nearestWire.first;
-    cathodeID[0] = hitInfo.nearestWire.second;
-    anodeID[1]   = hitInfo.nextNearestWire.first;
-    cathodeID[1] = hitInfo.nextNearestWire.second;
+    anodeID[0]   = hitInfo.nearestWire.first; // nearest anode wire ID
+    cathodeID[0] = hitInfo.nearestWire.second; // nearest cathode wire ID
+    anodeID[1]   = hitInfo.nextNearestWire.first; // next nearest anode wire ID
+    cathodeID[1] = hitInfo.nextNearestWire.second; // next nearest cathode wire ID
 
-    anodeDist[0]   = hitInfo.nearestDist.first;
-    cathodeDist[0] = hitInfo.nearestDist.second;
-    anodeDist[1]   = hitInfo.nextNearestDist.first;
-    cathodeDist[1] = hitInfo.nextNearestDist.second;
+    anodeDist[1]   = hitInfo.nextNearestDist.first; // distance to next nearest anode wire
+    cathodeDist[1] = hitInfo.nextNearestDist.second; // distance to next nearest cathode wire
 
+    if(IsDeadAnode(anodeID[0])) continue;
+    if(IsDeadCathode(cathodeID[0])) continue;
+
+    // SX3 hit channel info and depth fraction
     sx3ID = sx3->GetID();
+    qqqID = qqq->GetID();
+
+    if(IsDeadSX3(sx3ID)) continue;
+
+    anodeDist[0]   = hitInfo.nearestDist.first; // distance to nearest anode wire
+    cathodeDist[0] = hitInfo.nearestDist.second; // distance to nearest cathode wire
+    
+    //start HERE
     if( sx3ID >= 0 ){
       sx3Up    = sx3->GetChUp();
       sx3Dn    = sx3->GetChDn();
       sx3Bk    = sx3->GetChBk();
       sx3ZFrac = sx3->GetZFrac();
       
-      //Introduce uncertaity
-      // TVector3 hitPos = sx3->GetHitPos();
+      // apply intrinsic detector resolution to true SX3 hit position
+      // for no smearing comment out and use GetHitPos();
       TVector3 hitPos = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
 
       sx3X = hitPos.X();
       sx3Y = hitPos.Y();
       sx3Z = hitPos.Z();
 
+      // store track data for visualization if enabled
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+      // reconstruct track from PW readings + SX3 hit
       pw->CalTrack(hitPos, anodeID[0], cathodeID[0], false);
       reTheta = pw->GetTrackTheta() * TMath::RadToDeg();
       rePhi   = pw->GetTrackPhi() * TMath::RadToDeg();
 
+      // alternative track algorithm with uncertainty parameters
       pw->CalTrack2(hitPos, hitInfo, sigmaPW_A, sigmaPW_C, false);
       reTheta1 = pw->GetTrackTheta() * TMath::RadToDeg();
       rePhi1   = pw->GetTrackPhi() * TMath::RadToDeg();
 
       z0 = pw->GetZ0();
+      tree1->Fill();
+      //tree3->Fill();
 
-    }else{
+      // fill tree2 using the secondary proton from 21Na* decay
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      pw->FindWireID(vertex, dir2, false);
+      sx3->FindSX3Pos(vertex, dir2, false);
+      PWHitInfo hitInfo2 = pw->GetHitInfo();
+
+      anodeID2[0]   = hitInfo2.nearestWire.first;
+      cathodeID2[0] = hitInfo2.nearestWire.second;
+      anodeID2[1]   = hitInfo2.nextNearestWire.first;
+      cathodeID2[1] = hitInfo2.nextNearestWire.second;
+
+      anodeDist2[1]   = hitInfo2.nextNearestDist.first;
+      cathodeDist2[1] = hitInfo2.nextNearestDist.second;
+
+      if(IsDeadAnode(anodeID2[0]) || IsDeadCathode(cathodeID2[0])){
+        sx3ID2 = -1;
+      } else {
+        sx3ID2 = sx3->GetID();
+      }
+
+      if(sx3ID2 < 0 || IsDeadSX3(sx3ID2)){
+        sx3ID2 = -1;
+        sx3Up2 = -1;
+        sx3Dn2 = -1;
+        sx3Bk2 = -1;
+        sx3ZFrac2 = TMath::QuietNaN();
+        sx3X2 = TMath::QuietNaN();
+        sx3Y2 = TMath::QuietNaN();
+        sx3Z2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+      } else {
+        anodeDist2[0]   = hitInfo2.nearestDist.first;
+        cathodeDist2[0] = hitInfo2.nearestDist.second;
+        sx3Up2    = sx3->GetChUp();
+        sx3Dn2    = sx3->GetChDn();
+        sx3Bk2    = sx3->GetChBk();
+        sx3ZFrac2 = sx3->GetZFrac();
+        TVector3 hitPos2 = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+        sx3X2 = hitPos2.X();
+        sx3Y2 = hitPos2.Y();
+        sx3Z2 = hitPos2.Z();
+        pw->CalTrack(hitPos2, anodeID2[0], cathodeID2[0], false);
+        reTheta2 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi2   = pw->GetTrackPhi() * TMath::RadToDeg();
+        pw->CalTrack2(hitPos2, hitInfo2, sigmaPW_A, sigmaPW_C, false);
+        reTheta12 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi12   = pw->GetTrackPhi() * TMath::RadToDeg();
+        z02       = pw->GetZ0();
+      }
+
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+      qqqX = TMath::QuietNaN();
+      qqqY = TMath::QuietNaN();
+      qqqZ = TMath::QuietNaN();
+
+      tree2->Fill();
+
+    }else if (qqqID >= 0){
+      // handle QQQ hit case
       sx3Up = -1;
       sx3Dn = -1;
       sx3Bk = -1;
@@ -233,23 +596,97 @@ int main(int argc, char **argv){
       sx3Y = TMath::QuietNaN();
       sx3Z = TMath::QuietNaN();
 
-      // for( int i = 0; i < 12; i++){
-      //   sx3Index[i] = -1;
-      // }
+      reTheta  = TMath::QuietNaN();
+      rePhi    = TMath::QuietNaN();
+      reTheta1 = TMath::QuietNaN();
+      rePhi1   = TMath::QuietNaN();
+      z0       = TMath::QuietNaN();
+
+      qqqTb = Tb; // for simplicity, using the same kinetic energy for QQQ hit events, can be modified to simulate energy loss if desired
+      qqqTB = TB;
+
+      Tb = TMath::QuietNaN(); // mark kinetic energy as invalid for SX3 hit case
+      TB = TMath::QuietNaN();
+
+      TVector3 hitPos = qqq->GetHitPos();
+
+      qqqX = hitPos.X();
+      qqqY = hitPos.Y();
+      qqqZ = hitPos.Z();
+
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        //visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+
+      tree1->Fill();
+      //tree3->Fill();
+
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      qqq->FindQQQPos(vertex, dir2, false);
+
+      if(qqqID2 < 0){
+        qqqID2 = -1;
+        qqqX2 = TMath::QuietNaN();
+        qqqY2 = TMath::QuietNaN();
+        qqqZ2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+        anodeID2[0]   = TMath::QuietNaN(); // no valid anode wire for QQQ hit case
+        cathodeID2[0] = TMath::QuietNaN(); // no valid cathode wire for QQQ hit case
+        anodeID2[1]   = TMath::QuietNaN(); // no valid next nearest anode wire for QQQ hit case
+        cathodeID2[1] = TMath::QuietNaN(); // no valid next nearest cathode wire for QQQ hit case
+        anodeDist2[1]   = TMath::QuietNaN();
+        cathodeDist2[1] = TMath::QuietNaN();
+      }
+
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+
+      tree2->Fill();
+    }else{
+      // no valid SX3 hit: mark clearly invalid
+      sx3Up = -1;
+      sx3Dn = -1;
+      sx3Bk = -1;
+      sx3ZFrac = TMath::QuietNaN();
+
+      sx3X = TMath::QuietNaN();
+      sx3Y = TMath::QuietNaN();
+      sx3Z = TMath::QuietNaN();
 
       reTheta  = TMath::QuietNaN();
       rePhi    = TMath::QuietNaN();
-
       reTheta1 = TMath::QuietNaN();
       rePhi1   = TMath::QuietNaN();
-
       z0       = TMath::QuietNaN();
-
+      Tb       = TMath::QuietNaN(); // mark kinetic energy as invalid for no hit case
+      TB       = TMath::QuietNaN();
+      // fill tree with original data (no energy loss for these events)
+      //comment out tree fill for no hit case  
+      //tree1->Fill();
     }
 
-    tree->Fill();
-
     //#################################################################### Timer
+    // measure elapsed real time and print progress roughly every 10 sec
     clock.Stop("timer");
     Double_t time = clock.GetRealTime("timer");
     clock.Start("timer");
@@ -259,7 +696,7 @@ int main(int argc, char **argv){
         printf( "%10d[%2d%%]| %8.2f sec | expect: %5.1f min \n", i, TMath::Nint((i+1)*100./numEvent), time , numEvent*time/(i+1)/60);
         shown = 1;
       }
-    }else{
+    } else {
       if (fmod(time, 10) > 9 ){
         shown = 0;
       }
@@ -267,14 +704,78 @@ int main(int argc, char **argv){
 
   }
 
-  tree->Write();
-  int count = tree->GetEntries();
+  // write results to ROOT file and close
+  tree1->Write("", TObject::kOverwrite);
+  tree2->Write("", TObject::kOverwrite);
+  //tree3->Write("", TObject::kOverwrite);
+  int count1 = tree1->GetEntries();
+  int count2 = tree2->GetEntries();
+  //int count3 = tree3->GetEntries();
   saveFile->Close();
 
-  printf("=============== done. saved as %s. count(hit==1) : %d\n", saveFileName.Data(), count);
+  printf("=============== done. saved as %s. tree1 entries: %d, tree2 entries: %d\n", saveFileName.Data(), count1, count2);
+
+  if(enableVis){ // to enable visualization, run with 3rd argument "vis", e.g. "./anasenMC 1000 vis"
+    printf("Displaying geometry with %zu tracks from simulation\n", visTrackVertex.size());
+    
+    // Build full geometry with all wires
+    anasen->DrawAnasen(0, 23, 0, 23, -1, true);
+    
+    // Add all stored tracks to the geometry
+    TGeoManager *geom = anasen->GetGeoManager();
+    TGeoVolume *worldBox = anasen->GetWorldBox();
+    
+    if(geom && worldBox && visTrackVertex.size() > 0){
+      int trackNodeID = 500;  // start node IDs for tracks
+      
+      for(size_t iTrack = 0; iTrack < visTrackVertex.size(); ++iTrack){
+        TVector3 vertex = visTrackVertex[iTrack];
+        TVector3 dir = visTrackDir[iTrack];
+        TVector3 hitPos = visTrackHitPos[iTrack];
+        
+        double theta = dir.Theta() * TMath::RadToDeg();
+        double phi = dir.Phi() * TMath::RadToDeg();
+        
+        // Add a line marker at the vertex
+        TGeoVolume *startMarker = geom->MakeSphere("startMarker", 0, 0, 2.0);
+        startMarker->SetLineColor(kBlack);
+        worldBox->AddNode(startMarker, trackNodeID, 
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(), 
+                                          new TGeoRotation("rot", 0, 0, 0)));
+        trackNodeID++;
+        
+        // Add track line from vertex toward hit position
+        TGeoVolume *trackLine = geom->MakeTube("trackLine", 0, 0, 0.08, 150.0);
+        trackLine->SetLineColor(kBlue);
+        worldBox->AddNode(trackLine, trackNodeID,
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(),
+                                          new TGeoRotation("rotTrack", phi + 90, theta, 0)));
+        trackNodeID++;
+        
+        // Add hit position marker
+        TGeoVolume *hitMarker = geom->MakeSphere("hitMarker", 0, 0, 2.0);
+        hitMarker->SetLineColor(kRed);
+        worldBox->AddNode(hitMarker, trackNodeID,
+                         new TGeoCombiTrans(hitPos.X(), hitPos.Y(), hitPos.Z(),
+                                          new TGeoRotation("rotHit", 0, 0, 0)));
+        trackNodeID++;
+      }
+      
+      // Redraw geometry with all tracks
+      geom->CloseGeometry();
+      geom->SetVisLevel(4);
+      worldBox->Draw("ogle");
+    }
+    
+    if(app){
+      printf("Entering ROOT event loop\n");
+      app->Run();
+    }
+  }
 
   delete anasen;
 
+
   return 0;
 
 }

Armory/histcomp.C

@@ -0,0 +1,178 @@
+void histcomp() {
+    gROOT->SetBatch(kTRUE);
+
+    // Open file
+    TFile *f = new TFile("SimAnasen1.root");
+
+    // Get trees (MAKE SURE names are correct)
+    TTree *tree1 = (TTree*)f->Get("tree");
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    if (!tree1 || !tree2) {
+    printf("Error: could not find trees. Check names!\n");
+    return;
+    }
+
+    // Create output directory (overwrite-safe)
+    gSystem->Exec("mkdir -p plots");
+
+    // Get list of branches
+    TObjArray *branches = tree1->GetListOfBranches();
+    int nBranches = branches->GetEntries();
+    //int nBranches = 1;
+
+    // Loop over branches
+    for (int i = 0; i < nBranches; i++) {
+        TBranch *br = (TBranch*)branches->At(i);
+        TString name = br->GetName();
+
+        //printf("Processing branch: %s\n", name.Data());
+
+        // Create histograms (auto-range using Draw first)
+        TString h1name = "h1_" + name;
+        TString h2name = "h2_" + name;
+
+        // Temporary draw to get range
+        double min, max;
+
+        if(name == "T"){
+            //Get minimum value of T[0] and use as min  
+            min = tree2->GetMinimum("Tb");
+            max = tree1->GetMaximum("TB");
+        }else{
+
+            tree1->Draw(name, "", "goff");
+
+            min = fmin(tree1->GetMinimum(name),
+                    tree2->GetMinimum(name));
+
+            max = fmax(tree1->GetMaximum(name),
+                    tree2->GetMaximum(name));
+        }
+
+        //if (min == max) continue; // skip constant branches
+
+        // Expand range slightly
+        double margin = 0.1 * (max - min);
+        min -= margin;
+        max += margin;
+
+        TH1D *h1 = new TH1D(h1name, name, 100, min, max);
+        TH1D *h2 = new TH1D(h2name, name, 100, min, max);
+
+        // Fill histograms
+        if(name == "T"){
+
+            // Fill both array elements into same histogram
+            tree1->Draw("Tb>>+" + h1name, "", "goff");
+            tree1->Draw("TB>>+" + h1name, "", "goff");
+
+            tree2->Draw("Tb>>+" + h2name, "", "goff");
+            tree2->Draw("TB>>+" + h2name, "", "goff");
+
+        }else{
+
+            tree1->Draw(name + ">>" + h1name, "", "goff");
+            tree2->Draw(name + ">>" + h2name, "", "goff");
+
+        }
+
+        // Style
+        h1->SetLineColor(kRed);
+        h1->SetLineWidth(2);
+
+        h2->SetLineColor(kBlue);
+        h2->SetLineWidth(2);
+
+        // Normalize (optional but useful)
+        //if (h1->GetEntries() > 0) h1->Scale(1.0 / h1->GetEntries());
+        //if (h2->GetEntries() > 0) h2->Scale(1.0 / h2->GetEntries());
+
+        // Canvas
+        TCanvas *c = new TCanvas("c", name, 900, 600); //arguments are (name, title, width, height)
+
+        c->SetRightMargin(0.18);
+        c->Modified(); 
+        c->Update();
+
+        h1->SetTitle(name + ";"+name+";Counts");
+        h1->Draw("HIST");
+        h2->Draw("HIST SAME");
+
+        gPad->Update();
+
+        TPaveStats *st = (TPaveStats*)h1->FindObject("stats");
+
+        st->SetX1NDC(0.85); // New X start (left)
+        st->SetY1NDC(0.5); // New Y start (bottom)
+        st->SetX2NDC(0.98); // New X end (right)
+        st->SetY2NDC(0.8); // New Y end (top)
+        st->Draw();
+        gPad->Modified();
+        gPad->Update();
+
+
+        // Legend
+        TLegend *leg = new TLegend(0.65 + .2,0.75 + .1,0.88 + .1,0.88 + .1);
+        leg->AddEntry(h1, "tree1", "l");
+        leg->AddEntry(h2, "tree2", "l");
+        leg->Draw();
+        //to plot both as one histogram in root, can use tree2->Draw("T(0)"); for light particle and tree2->Draw("T(1)") for heavy particle
+        // Save plot (overwrite each run)
+        TString filename = "plots/" + name + ".png";
+        c->SaveAs(filename);
+        // Optional: save log plots as well
+
+        if (false) { // set to True to also save log plots
+            c->SetLogy(1);
+            h1->SetTitle(name + " (log);"+name+";Counts");
+            c->SaveAs("plots/" + name + "_logy.png");
+
+            c->SetLogy(0);
+            c->SetLogx(1);
+            h1->SetTitle(name + " (log);"+name+";Counts");
+            c->SaveAs("plots/" + name + "_logx.png");
+
+            // Clean up
+            delete c;
+            delete h1;
+            delete h2;
+        }
+
+
+
+    }
+
+    // dEb on y, SX3z on x
+    TH2D *h2d = new TH2D("h2d", "dEb vs SX3z;SX3z (cm);dEb (MeV)", 500, tree2->GetMinimum("sx3Z"), tree2->GetMaximum("sx3Z"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb")); //arguments are (name, title, xbins, xlow, xup, ybins, ylow, yup)
+    tree2->Draw("dEb:sx3Z>>h2d", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2d = new TCanvas("c2d", "dEb vs SX3z", 900, 600);
+    h2d->Draw("COLZ");
+    c2d->SaveAs("plots/dEb_vs_SX3z.png");
+
+    TH2D *h2z = new TH2D("h2z", "dEb vs z0", 500, tree2->GetMinimum("z0"), tree2->GetMaximum("z0"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:z0>>h2z", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2z = new TCanvas("c2z", "dEb vs z0", 900, 600);
+    h2z->Draw("COLZ");
+    c2z->SaveAs("plots/dEb_vs_z0.png");
+
+    TH2D *h2theta = new TH2D("h2theta", "dEb vs reTheta", 500, tree2->GetMinimum("reTheta"), tree2->GetMaximum("reTheta"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:reTheta>>h2theta", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2theta = new TCanvas("c2theta", "dEb vs reTheta", 900, 600);
+    h2theta->Draw("COLZ");
+    c2theta->SaveAs("plots/dEb_vs_reTheta.png");
+
+    TH2D *h2phi = new TH2D("h2phi", "dEb vs rePhi", 500, tree2->GetMinimum("rePhi"), tree2->GetMaximum("rePhi"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:rePhi>>h2phi", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2phi = new TCanvas("c2phi", "dEb vs rePhi", 900, 600);
+    h2phi->Draw("COLZ");
+    c2phi->SaveAs("plots/dEb_vs_rePhi.png");
+
+    TH2D *h2dE = new TH2D("h2dE", "dEb vs Tb", 500, tree2->GetMinimum("Tb"), tree2->GetMaximum("Tb"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:Tb>>h2dE", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2dE = new TCanvas("c2dE", "dEb vs Tb", 900, 600);
+    h2dE->Draw("COLZ");
+    c2dE->SaveAs("plots/dEb_vs_Tb.png");
+
+    printf("Done! Plots saved in ./plots/\n");
+}

Armory/macro.h

@@ -0,0 +1,56 @@
+#ifndef MACRO_H
+#define MACRO_H
+
+#define MaxNPorts 4   //for optical link
+#define MaxNBoards 4  //for both optical link and usb
+
+#define MaxNDigitizer MaxNPorts * MaxNBoards
+
+#define MaxRegChannel 16 
+#define MaxNChannels 64
+#define MaxRecordLength 0x3fff * 8 
+#define MaxSaveFileSize  1024 * 1024 * 1024 * 2
+
+#define MaxDisplayTraceTimeLength 20000 //ns
+#define ScopeUpdateMiliSec  200 // msec
+#define MaxNumberOfTrace  5   // in an event
+
+#define SETTINGSIZE 2048
+
+#define DAQLockFile "DAQLock.dat"
+#define PIDFile  "pid.dat"
+
+#include <sys/time.h> /** struct timeval, select() */
+
+inline unsigned int getTime_us(){
+  unsigned int time_us;
+  struct timeval t1;
+  struct timezone tz;
+  gettimeofday(&t1, &tz);
+  time_us = (t1.tv_sec) * 1000 * 1000 + t1.tv_usec;
+  return time_us;
+}
+
+#include <chrono>
+inline unsigned long long getTime_ns(){
+  std::chrono::high_resolution_clock::time_point currentTime = std::chrono::high_resolution_clock::now();
+  std::chrono::nanoseconds nanoseconds = std::chrono::duration_cast<std::chrono::nanoseconds>(currentTime.time_since_epoch());
+  return nanoseconds.count();
+}
+
+typedef unsigned short uShort;
+typedef unsigned int uInt;
+typedef unsigned long  uLong;
+typedef unsigned long long ullong;
+
+#define DebugMode 0 //process check, when 1, print out all function call
+
+// if DebugMode is 1, define DebugPrint() to be printf(), else, DebugPrint() define nothing
+#if DebugMode
+#define DebugPrint(fmt, ...) printf(fmt "::%s\n",##__VA_ARGS__, __func__);
+#else
+#define DebugPrint(fmt, ...)
+#endif
+
+
+#endif

Armory/run_script.C

@@ -0,0 +1,4 @@
+.L ANASEN_model.C
+.L anasenMS_root.cpp+
+ANASEN_model();
+Run(10);

Armory/vis_helpers.h

@@ -0,0 +1,61 @@
+#ifndef VIS_HELPERS_H
+#define VIS_HELPERS_H
+
+#include <TSystem.h>
+#include <TEvePointSet.h>
+#include <TTree.h>
+#include <vector>
+#include <mutex>
+
+static TEvePointSet* gVisPts = nullptr;
+static std::mutex gVisMutex;
+
+// Recommended: call once after opening TEve and adding a point set to gEve
+inline void SetVisPointSet(TEvePointSet* pts) { gVisPts = pts; }
+
+inline void UpdateVisPointSet(const std::vector<double>& x,
+                              const std::vector<double>& y,
+                              const std::vector<double>& z)
+{
+  if(!gVisPts) return;
+  std::lock_guard<std::mutex> lk(gVisMutex);
+  gVisPts->Reset();
+  size_t n = std::min({x.size(), y.size(), z.size()});
+  for(size_t i=0; i<n; ++i) gVisPts->SetNextPoint(x[i], y[i], z[i]);
+  if(gEve) {
+    gEve->Redraw3D();
+    gSystem->ProcessEvents();
+  }
+}
+
+// Fill a tree with pointlists (one entry per event); must have branches defined once by caller
+inline void RecordTreeXYZ(TTree* outTree,
+                           const std::vector<double>& x,
+                           const std::vector<double>& y,
+                           const std::vector<double>& z)
+{
+  if(!outTree) return;
+  static std::vector<double> tx, ty, tz;
+  tx = x;
+  ty = y;
+  tz = z;
+
+  if(outTree->GetBranch("x") == nullptr) outTree->Branch("x", &tx);
+  if(outTree->GetBranch("y") == nullptr) outTree->Branch("y", &ty);
+  if(outTree->GetBranch("z") == nullptr) outTree->Branch("z", &tz);
+
+  // Do NOT call SetBranchAddress() for the branch we are filling.
+  outTree->Fill();
+  outTree->GetCurrentFile()->Flush();
+}
+
+inline void PushEventAndRecord(const std::vector<double>& x,
+                               const std::vector<double>& y,
+                               const std::vector<double>& z,
+                               TTree* outTree = nullptr)
+{
+  if(outTree) RecordTreeXYZ(outTree, x, y, z);
+  UpdateVisPointSet(x,y,z);
+}
+
+#endif // VIS_HELPERS_H

Armory/vis_inproc.cpp

@@ -0,0 +1,65 @@
+//In-ROOT sim data
+
+// vis_inproc.cpp
+#include <TApplication.h>
+#include <TGeoManager.h>
+#include <TEveManager.h>
+#include <TEvePointSet.h>
+#include <TSystem.h>
+#include <TRandom3.h>
+#include <thread>
+#include <chrono>
+#include <vector>
+#include <iostream>
+
+void runSimulationAndUpdate(TEvePointSet* pts){
+  TRandom3 rnd(0);
+  for(int ev=0; ev<10000; ++ev){
+    pts->Reset();
+    int n = 100;
+    for(int i=0;i<n;++i){
+      double x = rnd.Uniform(-50,50);
+      double y = rnd.Uniform(-50,50);
+      double z = rnd.Uniform(-50,50);
+      pts->SetNextPoint(x,y,z);
+    }
+    gEve->Redraw3D();
+    gSystem->ProcessEvents();
+    std::this_thread::sleep_for(std::chrono::milliseconds(100));
+  }
+}
+
+void StartVis(const char* geomfile=nullptr){
+  int argc=0; char** argv=nullptr;
+  TApplication app("app",&argc,argv);
+  if(geomfile) TGeoManager::Import(geomfile);
+  TEveManager::Create();
+  TEvePointSet *pts = new TEvePointSet("hits");
+  gEve->AddElement(pts);
+  // runSimulationAndUpdate(pts);  // or leave update API to caller
+  app.Run();
+}
+
+int main(int argc, char** argv){
+  TApplication app("app",&argc,argv);
+
+  if(argc>1) TGeoManager::Import(argv[1]);
+
+  TEveManager::Create();
+
+  TEvePointSet *pts = new TEvePointSet("hits");
+  pts->SetMarkerStyle(20);
+  pts->SetMarkerSize(1.2);
+  pts->SetMarkerColor(kRed);
+  gEve->AddElement(pts);
+
+  // Option A: run simulation in same thread but yield to event loop inside the sim
+  runSimulationAndUpdate(pts);
+
+  // Option B: run sim in a separate thread (only if sim avoids ROOT globals)
+  // std::thread simThread(runSimulationAndUpdate, pts);
+  // simThread.detach();
+
+  app.Run();
+  return 0;
+}

BatchProcess.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+#parallel -j 6 echo ./ProcessRun.sh {1} 2000 0 ::: {020..400}
+
+#parallel --results log/log_{}.txt --ctag -j 6 ./ProcessRun.sh {1} 2000 0 ::: {020..400} # for 17F
+
+parallel --results log/log_{}.txt --ctag -j 6 ./ProcessRun.sh {1} 2000 0 ::: {001..021}