diff --git a/#AraSim.cc# b/#AraSim.cc#
new file mode 100644
index 00000000..17e9f62a
--- /dev/null
+++ b/#AraSim.cc#
@@ -0,0 +1,829 @@
+// ROOT includes
+#include "TFile.h"
+#include "TRandom3.h" 
+#include "TTree.h"
+
+// AraSim includes
+//vector and position must be first
+#include "Vector.h"
+#include "Position.h"
+
+#include "Constants.h"
+#include "counting.hh"
+#include "Detector.h"
+#include "EarthModel.h"
+#include "Efficiencies.h"
+#include "Event.h"
+#include "IceModel.h"
+#include "Primaries.h"
+#include "Ray.h"
+#include "Report.h"
+#include "RaySolver.h"
+#include "secondaries.hh"
+#include "Settingsude "signal.hh"
+#include "Spectra.h"
+#include "Tools.h"
+#include "Trigger.h"
+
+using namespace std;
+
+#ifdef ARA_UTIL_EXISTS
+    #include "UsefulIcrrStationEvent.h"
+    ClassImp(UsefulIcrrStationEvent);
+    #include "UsefulAtriStationEvent.h"
+    ClassImp(UsefulAtriStationEvent);
+#endif
+
+class EarthModel; //class
+
+void test();
+
+string outputdir="outputs";
+
+int main(int argc, char **argv) {   // read setup.txt file
+    
+    Settings *settings1 = new Settings();
+
+    cout<<"\n\tDefault values!"<<endl;
+    cout<<"NNU : "<<settings1->NNU<<endl;
+    cout<<"ICE_MODEL : "<<settings1->ICE_MODEL<<endl;
+    cout<<"NOFZ : "<<settings1->NOFZ<<endl;
+    cout<<"CONSTANTICETHICKNESS : "<<settings1->CONSTANTICETHICKNESS<<endl;
+    cout<<"FIXEDELEVATION : "<<settings1->FIXEDELEVATION<<endl;
+    cout<<"MOOREBAY : "<<settings1->MOOREBAY<<endl;
+    cout<<"EXPONENT : "<<settings1->EXPONENT<<endl;
+    cout<<"DETECTOR : "<<settings1->DETECTOR<<endl;
+
+    //string setupfile = "setup.txt";
+    string setupfile;
+    string run_no;
+    if (argc<2) { // no setup file input, use default
+        setupfile = "setup.txt";
+        cout<<"setupfile : "<<setupfile<<endl;
+    }
+    else if (argc > 1) { // read file!!
+        setupfile = string( argv[1] );
+        cout<<"setupfile : "<<setupfile<<endl;
+    }
+    if (argc > 2) { // read file!!
+        run_no = string( argv[2] );
+        cout<<"run number : "<<run_no<<endl;
+    }
+    if (argc > 3) { // read file!!
+        outputdir = string( argv[3] );
+        if(outputdir[outputdir.size()-1]=='/') outputdir=outputdir.substr(0,outputdir.size()-1); // make sure outputdir doesn't have a / at the end
+        cout<<"outputdir : "<<outputdir<<endl;
+    }
+    // else { // no mode for argc > 2!
+    //  cout<<"too many info! just use default setup.txt file!"<<endl;
+    //  setupfile = "setup.txt";
+    // }
+
+    settings1->ReadFile(setupfile);
+    cout<<"Read "<<setupfile<<" file!"<<endl;
+
+    cout<<"\n\tNew values!"<<endl;
+    cout<<"NNU : "<<settings1->NNU<<endl;
+    cout<<"ICE_MODEL : "<<settings1->ICE_MODEL<<endl;
+    cout<<"NOFZ : "<<settings1->NOFZ<<endl;
+    cout<<"CONSTANTICETHICKNESS : "<<settings1->CONSTANTICETHICKNESS<<endl;
+    cout<<"FIXEDELEVATION : "<<settings1->FIXEDELEVATION<<endl;
+    cout<<"MOOREBAY : "<<settings1->MOOREBAY<<endl;
+    cout<<"EXPONENT : "<<settings1->EXPONENT<<endl;
+    cout<<"DETECTOR : "<<settings1->DETECTOR<<endl;
+    cout<<"POSNU_RADIUS : "<<settings1->POSNU_RADIUS<<endl;
+    cout << "EVENT_GENERATION_MODE: " << settings1->EVENT_GENERATION_MODE << endl;
+    // cout << "EVENT_NUM: " << settings1->EVENT_NUM << endl;
+
+    if (settings1->EVENT_GENERATION_MODE == 1){
+        // string evtfile = "eventReadIn.txt";
+        string evtfile = string(argv[argc - 1]);
+        settings1->ReadEvtFile(evtfile);
+        cout<<"Read "<< evtfile <<" file!"<<endl;
+        cout << "EVID    NUFLAVORINT    NUBAR    PNU    CURRENTINT    IND_POSNU_R    IND_POSNU_THETA    IND_POSNU_PHI    IND_NNU_THETA    IND_NNU_PHI    ELAST" << endl;
+        for (int i = 0; i < settings1->NNU; i++){
+            cout << settings1->EVID[i] << "    " << settings1->NUFLAVORINT[i] << "    " << settings1->NUBAR[i] << "    " << settings1->PNU[i] << "    " << settings1->CURRENTINT[i] << "    " << settings1->IND_POSNU_R[i] << "    " << settings1->IND_POSNU_THETA[i] << "    " << settings1->IND_POSNU_PHI[i] << "    " << settings1->IND_NNU_THETA[i] << "    " << settings1->IND_NNU_PHI[i] << "    " << settings1->ELAST[i] << endl;
+        }
+    }
+    // set gRandom as TRandom3 when settings1->RANDOM_MODE = 1
+    if (settings1->RANDOM_MODE == 1) {
+        // test TRandom3
+        TRandom3 *test_randm3 = new TRandom3 (0);
+        gRandom = test_randm3;
+    } else {
+        gRandom->SetSeed(settings1->SEED + atoi(run_no.c_str() ) );
+            
+    }
+    //cout<<"first random from TRandom3 : "<<test_randm3->Rndm()<<"\n";
+    cout<<"first random : "<<gRandom->Rndm()<<"\n";
+
+    // IceModel *icemodel=new IceModel(ICE_MODEL + NOFZ*10,CONSTANTICETHICKNESS * 1000 + CONSTANTCRUST * 100 + FIXEDELEVATION * 10 + 0,MOOREBAY);// creates Antarctica ice model
+    IceModel *icemodel=new IceModel(settings1->ICE_MODEL + settings1->NOFZ*10,settings1->CONSTANTICETHICKNESS * 1000 + settings1->CONSTANTCRUST * 100 + settings1->FIXEDELEVATION * 10 + 0,settings1->MOOREBAY);// creates Antarctica ice model
+    // IceModel inherits from EarthModel  
+
+    cout<<endl;
+    cout<<"Surface at (log:0, lat:0) : "<<icemodel->Surface(0., 0.)<<endl;
+    cout<<"SurfaceAboveGeoid at (log:0, lat:0) : "<<icemodel->SurfaceAboveGeoid(0., 0.)<<endl;
+    
+    // Detector *detector=new Detector(settings1, icemodel); // builds antenna array, 0 for testbed
+    Detector *detector=new Detector(settings1, icemodel, setupfile ); // builds antenna array, 0 for testbed
+    cout<<"end calling detector"<<endl;
+    // Detector *detector=new Detector(settings1->DETECTOR); // builds antenna array, 0 for testbed
+
+    Trigger *trigger=new Trigger(detector, settings1); // builds the trigger  
+    // Efficiencies *efficiencies=new Efficiencies(detector->getnRx(),outputdir); // keeps track of efficiencies at each stage of the simulation
+    Efficiencies *efficiencies=new Efficiencies(100,outputdir); // keeps track of efficiencies at each stage of the simulation
+    cout<<"called Efficiencies"<<endl;
+    
+    Spectra *spectra=new Spectra(settings1->EXPONENT); // gets library (or whatever) of neutrino spectra
+    cout<<"called Spectra"<<endl;
+
+    Ray *ray = new Ray(); // construct Ray class
+    cout<<"called Ray"<<endl;
+    
+
+    // test PickUnbiased in IceModel.
+    Counting *count1 = new Counting();
+    cout<<"called Counting"<<endl;
+
+    Primaries *primary1 = new Primaries();
+    cout<<"called Primaries"<<endl;
+
+    int whichray = 0; // for test
+    //--------------------------------------------------
+    //   Interaction *interaction1=new Interaction("nu",primary1,settings1,whichray,count1);
+    //   cout<<"called Interaction1"<<endl;
+    //-------------------------------------------------- 
+
+    Event *event = new Event();
+    cout<<"called Event"<<endl;
+
+    //Report *report = new Report(detector, settings1);
+    Report *report = new Report();
+    cout<<"called Evt"<<endl;
+
+    TFile *AraFile;
+    if (argc > 2) {
+        AraFile=new TFile((outputdir+"/AraOut."+setupfile.substr(setupfile.find_last_of("/")+1)+".run"+run_no+".root").c_str(),"RECREATE","ara");
+    }
+    else {
+        AraFile=new TFile((outputdir+"/AraOut.root").c_str(),"RECREATE","ara");
+    }
+
+    TTree *AraTree=new TTree("AraTree","AraTree");    // for single entry
+    TTree *AraTree2=new TTree("AraTree2","AraTree2"); //for many entries
+    cout<<"assign AraFile, AraTrees"<<endl;
+
+    AraTree->Branch("detector",&detector);
+    cout<<"branch detector"<<endl;
+    AraTree->Branch("icemodel",&icemodel);
+    cout<<"branch icemodel"<<endl;
+    AraTree->Branch("trigger",&trigger);
+    cout<<"branch trigger"<<endl;
+    AraTree->Branch("settings",&settings1);
+    cout<<"branch settings"<<endl;
+    AraTree->Branch("spectra",&spectra);
+    cout<<"branch spectra"<<endl;
+    AraTree2->Branch("event",&event);
+    cout<<"branch Evt"<<endl;
+    AraTree2->Branch("report",&report);
+    cout<<"branch report"<<endl;
+
+    cout<<"finish tree assign"<<endl;
+
+
+    RaySolver *raysolver = new RaySolver();
+    cout<<"called RaySolver"<<endl;
+
+    cout << "Make output file that is readable by AraRoot" << endl;
+
+    #ifdef ARA_UTIL_EXISTS
+        UsefulIcrrStationEvent *theIcrrEvent =0;
+        UsefulAtriStationEvent *theAtriEvent =0;
+    
+
+        TTree *eventTree;
+
+        double weight = 0.;
+        eventTree = new TTree("eventTree","Tree of ARA Events");
+        eventTree->Branch("UsefulIcrrStationEvent", &theIcrrEvent);
+        eventTree->Branch("UsefulAtriStationEvent",&theAtriEvent);
+        eventTree->Branch("weight", &weight);
+
+        /*
+        UsefulIcrrStationEvent *theIcrrEventArray[3];
+        for (int i = 0; i < 3; i++){
+            theIcrrEvent[i] = 0;
+        }
+        UsefulAtriStationEvent *theAtriEventArray[38];
+        for (int i = 0; i < 38; i++){
+            theAtriEvent[i] = 0;
+        }
+        */
+
+
+        /*
+        TTree *eventTree0;
+        eventTree0 = new TTree("eventTree0","Tree of Station 0 ARA Events");
+        eventTree0->Branch("UsefulIcrrStationEvent",&theIcrrEventArray[0]);
+        TTree *eventTree1;
+        eventTree1 = new TTree("eventTree1","Tree of Station 1 ARA Events");
+        eventTree1->Branch("UsefulAtriStationEvent",&theAtriEventArray[1]);
+        TTree *eventTree2;
+        eventTree2 = new TTree("eventTree2","Tree of Station 2 ARA Events");
+        eventTree2->Branch("UsefulAtriStationEvent",&theAtriEventArray[2]);
+        TTree *eventTree3;
+        eventTree3 = new TTree("eventTree3","Tree of Station 3 ARA Events");
+        eventTree3->Branch("UsefulAtriStationEvent",&theAtriEventArray[3]);
+        */
+    #endif
+
+
+    cout<<"will call secondaries"<<endl;
+    Secondaries *sec1 = new Secondaries (settings1);
+    cout<<"will call signal"<<endl;
+    // Signal *signal = new Signal;
+    Signal *signal = new Signal (settings1);
+    signal->SetMedium(0);   // set medium as ice
+    cout<<"finish calling secondaries and signal"<<endl;
+
+    // before start looping events set noise values (this case, thermal)
+    trigger->SetMeanRmsDiode(settings1, detector, report);
+
+    if (settings1->NOISE_WAVEFORM_GENERATE_MODE == 0) {// noise waveforms will be generated for each evts
+        trigger->ClearNoiseWaveforms();
+    }
+
+    // now in Trigger class, there will be meandiode, rmsdiode values for noise (we need this for trigger later)
+
+    double max_dt = 0.; // max arrival time difference
+
+    int Total_Global_Pass = 0;  // total global trigger passed number 
+    double Total_Weight = 0.;
+    double Total_Probability = 0.;
+
+
+    /*
+
+    TCanvas *cFull_window = new TCanvas("cFull_window","A Simple Graph Example",200,10,10000,11200);
+    cFull_window->Divide(1,16);
+
+    TGraph *g_Full_window;
+
+    TGraph *G_V_threshold_diode;
+    G_V_threshold_diode = new TGraph(2, threshold_x, threshold_y);
+
+    TCanvas *cFull_window_V = new TCanvas("cFull_window_V","A Simple Graph Example",200,10,3200,2400);
+    cFull_window_V->Divide(4,4);
+
+    TGraph *g_Full_window_V;
+
+    */
+
+    double x_V[settings1->NFOUR/2];
+    double y_V[settings1->NFOUR/2];
+
+
+
+    double xbin[settings1->DATA_BIN_SIZE];
+    for (int i=0; i<settings1->DATA_BIN_SIZE; i++) {
+        xbin[i] = i;
+    }
+
+    double threshold_y[2];
+    double threshold_x[2];
+
+    threshold_x[0] = 0.;
+    threshold_x[1] = (double)settings1->DATA_BIN_SIZE-1.;
+    threshold_y[0] = (trigger->rmsdiode) * (trigger->powerthreshold);
+    threshold_y[1] = (trigger->rmsdiode) * (trigger->powerthreshold);
+
+    cout<<"powerthreshold : "<<trigger->powerthreshold<<endl;
+
+    int check_station_DC;
+
+    ofstream TrigWind;
+    TrigWind.open("outputs/TrigWindowStudy.txt");
+        
+        
+    // for (int iTrigWind = 10; iTrigWind < 201; iTrigWind = iTrigWind+10){
+        
+    //  double TRIG_WINDOW_Size = double (iTrigWind * 1.0E-9);
+    //  settings1->TRIG_WINDOW = TRIG_WINDOW_Size;
+                
+    Total_Global_Pass = 0;
+    cout<<"begin looping events!!"<<endl;
+
+
+    double pre_posnu_x;
+    double pre_posnu_y;
+    double pre_posnu_z;
+
+    double cur_posnu_x;
+    double cur_posnu_y;
+    double cur_posnu_z;
+
+
+    cout << "Calpulser_on: " << settings1->CALPULSER_ON << endl;
+
+    // test Detector set correctly
+    cout<<"number of stations : "<<detector->params.number_of_stations << endl;
+    cout<<"total number of antennas : "<<detector->params.number_of_antennas << endl;
+    int ch_count = 0;
+    for (int i=0; i<detector->params.number_of_stations; i++) {
+        for (int j=0; j<detector->stations[i].strings.size(); j++) {
+            for (int k=0; k<detector->stations[i].strings[j].antennas.size(); k++) {
+                ch_count++;
+                cout<<"station["<<i<<"].strings["<<j<<"].antennas["<<k<<"] no_ch:"<<ch_count<<endl;
+            }
+        }
+    }
+
+
+
+                
+    // check if settings have to compatibility problems
+    // if there's any, stop AraSim
+    int settings_compatibility_error = settings1->CheckCompatibilities(detector);
+    if (settings_compatibility_error > 0) {
+        cerr<<"There are "<< settings_compatibility_error<<" errors from settings. Check error messages."<<endl;
+        return -1;
+    }
+        
+    #ifndef ARA_UTIL_EXISTS
+        if (settings1->DETECTOR == 3 && settings1->READGEOM == 1){
+            cerr << "ERROR::InstalledStation geometry not available without AraRoot installation!" << endl;
+            return -1;
+        }
+    #endif
+
+
+    // test autoflush
+    // AraTree2->SetAutoFlush(0);
+
+    // reset accumulative trig search bin info 
+    settings1->ACCUM_TRIG_SEARCH_BINS_STATION0 = 0.;
+
+    int nuLimit =0;
+    if (settings1->EVENT_GENERATION_MODE == 1){ //event mode read in different single events
+        nuLimit = settings1->NNU;
+    }
+    else if (settings1->ONLY_PASSED_EVENTS == 1){
+        nuLimit = settings1->NNU_PASSED;
+    }
+    else {
+        nuLimit = settings1->NNU;
+    }
+    // cout << "nuLimit: " << nuLimit << endl; 
+    int inu = 0;
+    int Events_Thrown = 0;
+    int Events_Passed = 0;
+    // for (int inu=0;inu<settings1->NNU;inu++) { // loop over neutrinos
+    while (inu < nuLimit){
+        // cout << "inu: " << inu << endl; 
+        check_station_DC = 0;
+        check_station_DC = 0;
+        if ( settings1->DEBUG_MODE_ON==0 ) {
+            std::cerr<<"*";
+            if ( Events_Thrown%100 == 0 )
+                cout<<"Thrown "<<Events_Thrown<<endl;
+        }
+
+        // event = new Event ( settings1, spectra, primary1, icemodel, detector, signal, sec1 );
+        event = new Event ( settings1, spectra, primary1, icemodel, detector, signal, sec1, Events_Thrown );
+        event->inu_passed = -1;
+                
+        report = new Report(detector, settings1);
+                        
+        #ifdef ARA_UTIL_EXISTS
+            theIcrrEvent = new UsefulIcrrStationEvent();
+            theAtriEvent = new UsefulAtriStationEvent();
+        #endif
+
+
+        // go further only if we picked up usable posnu
+        if (event->Nu_Interaction[0].pickposnu>0) {
+
+            /*
+            if (settings1->NOISE_WAVEFORM_GENERATE_MODE == 0) {// noise waveforms will be generated for each evts
+                trigger->GetNewNoiseWaveforms(settings1, detector, report);
+            }
+            */
+
+
+            //--------------------------------------------------
+            // cout<<"inu : "<<inu<<endl;
+            // cout<<"event->pnu : "<<event->pnu<<endl;
+            // cout<<"posnu : ";
+            // event->Nu_Interaction[0].posnu.Print();
+            // cout<<"nnu : ";
+            // event->Nu_Interaction[0].nnu.Print();
+            // cout<<"event->n_interactions : "<<event->n_interactions<<endl;
+            // cout<<"nu_flavor : "<<event->nuflavor<<endl;
+            // cout<<"event->Nu_Interaction[0].vmmhz1m[0] : "<<event->Nu_Interaction[0].vmmhz1m[0]<<endl;
+            // cout<<"pickposnu : "<<event->Nu_Interaction[0].pickposnu<<endl;
+            //-------------------------------------------------- 
+
+            // connect Interaction class (nu interaction with ice) and Detector class (detector properties and layout)
+            // save signal, noise at each antennas to Report class
+            //report->Connect_Interaction_Detector (event, detector, raysolver, signal, icemodel, settings1, trigger);
+
+            //report->Connect_Interaction_Detector (event, detector, raysolver, signal, icemodel, settings1, trigger, theEvent);
+            report->Connect_Interaction_Detector (event, detector, raysolver, signal, icemodel, settings1, trigger, Events_Thrown);
+            //report->Connect_Interaction_Detector (event, detector, raysolver, signal, icemodel, settings1, trigger, theEvent, Events_Thrown);
+
+            #ifdef ARA_UTIL_EXISTS
+                if (settings1->DATA_LIKE_OUTPUT !=0){
+                    int stationID;
+                    int stationIndex;
+                    if (settings1->DETECTOR == 4){
+                        stationID = settings1->DETECTOR_STATION;
+                        stationIndex = 0;
+                    } else {
+                        stationID = 0;
+                        stationIndex = 0;
+                    }
+
+                    if (report->stations[stationIndex].Global_Pass) {
+                        // report->MakeUsefulEvent(detector, settings1, trigger, stationID, stationIndex, theIcrrEvent);
+                        cout << endl << "Making useful event" << endl;
+                        report->MakeUsefulEvent(detector, settings1, trigger, stationID, stationIndex, theAtriEvent);
+                        /*
+                        for (int i_chan = 0; i_chan< 16; i_chan++){
+                            int elecChan = AraGeomTool::Instance()->getElecChanFromRFChan(i_chan, stationID);
+                            int string_i = detector->getStringfromArbAntID( stationIndex, i_chan);
+                            int antenna_i = detector->getAntennafromArbAntID( stationIndex, i_chan);
+                            cout << "Output: " << elecChan << " : " << theAtriEvent->fTimes[elecChan][1] <<  " : " << report->stations[stationIndex].strings[string_i].antennas[antenna_i].time_mimic[1] << endl;
+                        }
+                        */
+                    }
+                    weight = event->Nu_Interaction[0].weight;
+                }
+                // cout << "weight: " << weight <<endl;    
+            #endif
+                     
+            report->ClearUselessfromConnect(detector, settings1, trigger);
+            for(int i=0;i<event->Nu_Interaction.size(); i++)
+                event->Nu_Interaction[i].clear_useless(settings1);
+
+            // test if posnu is exactly same in calpulser mode
+            if (settings1->CALPULSER_ON == 1) {
+                cur_posnu_x = event->Nu_Interaction[0].posnu.GetX();
+                cur_posnu_y = event->Nu_Interaction[0].posnu.GetY();
+                cur_posnu_z = event->Nu_Interaction[0].posnu.GetZ();
+                // cout<<"posnu x:"<<cur_posnu_x<<" y:"<<cur_posnu_y<<" z:"<<cur_posnu_z<<endl;
+                if (inu>0) {
+                    if (pre_posnu_x==cur_posnu_x && pre_posnu_y==cur_posnu_y && pre_posnu_z==cur_posnu_z) {
+                    }
+                    else cout<<"posnu location changed!"<<endl;
+                }
+                pre_posnu_x = event->Nu_Interaction[0].posnu.GetX();
+                pre_posnu_y = event->Nu_Interaction[0].posnu.GetY();
+                pre_posnu_z = event->Nu_Interaction[0].posnu.GetZ();
+            }
+
+            for (int i=0; i<detector->params.number_of_stations; i++) {
+                #ifdef ARA_UTIL_EXISTS
+                    if (settings1->DATA_LIKE_OUTPUT != 0){
+                        if (settings1->DETECTOR == 3 && i == 0)
+                            { theIcrrEvent->numRFChans = 14; }
+                        else if (settings1->DETECTOR == 4 && settings1->DETECTOR_STATION == 0)
+                            { theIcrrEvent->numRFChans = 14; }
+                        else { 
+                            theAtriEvent->fNumChannels = 20; 
+                            theIcrrEvent->numRFChans = 16; 
+                        }
+                    }
+                #endif
+                     
+                if (max_dt < report->stations[i].max_arrival_time - report->stations[i].min_arrival_time)
+                    max_dt = report->stations[i].max_arrival_time - report->stations[i].min_arrival_time;
+                // check the total global trigger passed
+                if (report->stations[i].Global_Pass) {
+                    cout<<"\nGlobal_Pass : "<<report->stations[i].Global_Pass<<" evt : "<<inu<<" added weight : "<<event->Nu_Interaction[0].weight<<endl;
+                    if ( check_station_DC == 0) { // count trigger pass only once per event
+                             
+                        Total_Global_Pass ++;
+                        Total_Weight += event->Nu_Interaction[0].weight;
+                        Total_Probability += event->Nu_Interaction[0].probability;
+                             
+                        // test increment weight
+                        if (settings1->INTERACTION_MODE==1) {
+                            count1->incrementEventsFound( event->Nu_Interaction[0].weight, event );
+                        }
+                        else if (settings1->INTERACTION_MODE==0) {
+                            count1->incrementEventsFound( event->Nu_Interaction[0].probability, event );
+                        }
+                        else if (settings1->INTERACTION_MODE==3) {
+                            count1->incrementEventsFound( event->Nu_Interaction[0].probability, event );
+                        }
+                        else if (settings1->INTERACTION_MODE==4) {
+                            count1->incrementEventsFound( event->Nu_Interaction[0].weight, event );
+                        }    
+                    }
+                    check_station_DC++;
+                    event->inu_passed = Events_Passed; 
+                }
+            }
+
+            /*
+            AraTree2->Fill();   //fill interaction every events
+            // for 1, save all events whether passed trigger or not
+            if (settings1->DATA_LIKE_OUTPUT==2) {
+                //theEvent = &report->theUsefulEvent;
+                eventTree->Fill();
+            }
+            // for 0, save events which passed trigger
+            else if (settings1->DATA_LIKE_OUTPUT==1) {
+                //if ( Global_Pass_Flag == 1 ) {
+                if ( check_station_DC > 0 ) {
+                    //theEvent = &report->theUsefulEvent;
+                    eventTree->Fill();
+                }
+            }
+            theEvent = NULL;
+
+            delete theEvent;
+            */
+
+            settings1->ACCUM_TRIG_SEARCH_BINS_STATION0 += report->stations[0].total_trig_search_bin;
+        } // if pickposnu > 0
+        else {
+            //cout<<"pickposnu : "<<event->Nu_Interaction[0].pickposnu<<endl;
+            report->delete_all();
+            event->delete_all();
+        }
+
+
+        // test FILL_TREE_MODE
+        if (settings1->FILL_TREE_MODE==0) { // fill event event  
+            AraTree2->Fill();   //fill interaction every events
+            #ifdef ARA_UTIL_EXISTS
+                // for 1, save all events whether passed trigger or not
+                if (settings1->DATA_LIKE_OUTPUT==2) {
+                    // theEvent = &report->theUsefulEvent;
+                    eventTree->Fill();
+                }
+                // for 0, save events which passed trigger
+                else if (settings1->DATA_LIKE_OUTPUT==1) {
+                    if ( check_station_DC > 0 ) {
+                        // theEvent = &report->theUsefulEvent;
+                        eventTree->Fill();
+                    }
+                }
+            #endif
+        }
+        else if (settings1->FILL_TREE_MODE==1) { // fill only usable posnu event 
+            if (event->Nu_Interaction[0].pickposnu>0) {
+                AraTree2->Fill();   //fill interaction every events
+                #ifdef ARA_UTIL_EXISTS
+                    // for 1, save all events whether passed trigger or not
+                    if (settings1->DATA_LIKE_OUTPUT==2) {
+                        // theEvent = &report->theUsefulEvent;
+                        eventTree->Fill();
+                    }
+                    // for 0, save events which passed trigger
+                    else if (settings1->DATA_LIKE_OUTPUT==1) {
+                        if ( check_station_DC > 0 ) {
+                            //theEvent = &report->theUsefulEvent;
+                            eventTree->Fill();
+                        }
+                    }
+                #endif
+            }
+        }
+        else if (settings1->FILL_TREE_MODE==2) { // fill only triggered event    
+            if (check_station_DC>0) {
+                AraTree2->Fill();   //fill interaction every events
+                #ifdef ARA_UTIL_EXISTS
+                    // for 1, save all events whether passed trigger or not
+                    if (settings1->DATA_LIKE_OUTPUT==2) {
+                        //theEvent = &report->theUsefulEvent;
+                        eventTree->Fill();
+                    }
+                    // for 0, save events which passed trigger
+                    else if (settings1->DATA_LIKE_OUTPUT==1) {
+                        if ( check_station_DC > 0 ) {
+                            //theEvent = &report->theUsefulEvent;
+                            eventTree->Fill();
+                        }
+                    }
+                #endif
+            }
+        }
+        if (settings1->EVENT_GENERATION_MODE == 1){
+            inu++;
+        }
+        else if (settings1->ONLY_PASSED_EVENTS == 1){
+            if (check_station_DC > 0){
+                inu++;
+            }
+        }
+        else {
+            inu++;
+        }
+        if (check_station_DC > 0){
+            Events_Passed++;
+        }
+        Events_Thrown++;
+             
+
+        //theEvent = NULL;
+
+        /*
+        if (settings1->NOISE_WAVEFORM_GENERATE_MODE == 0) {// noise waveforms will be generated for each evts
+            // remove noise waveforms for next evt
+            rigger->ClearNoiseWaveforms();
+        }
+        */
+
+        // if(inu==nuLimit){
+        //      cout<<endl<<"sizeof: Report= "<<sizeof(*report)<<"  station= "<<sizeof(report->stations[0])<<"  antenna= "<<sizeof(report->stations[0].strings[0].antennas[0])<<endl;
+        //      cout<<"sizeof: Event= "<<sizeof(*event)<<" Interaction= "<<sizeof(event->Nu_Interaction[0])<<"  TOTAL SIZE= "<<sizeof(*report)+sizeof(*event)+sizeof(report->stations[0])+16*sizeof(report->stations[0].strings[0].antennas[0])+sizeof(event->Nu_Interaction[0])<<endl;
+        // }
+
+        delete event;
+        delete report;
+        #ifdef ARA_UTIL_EXISTS
+            delete theIcrrEvent;
+            delete theAtriEvent;
+        #endif
+
+    } // end loop over neutrinos
+
+    settings1->NNU = Events_Thrown;
+    settings1->NNU_PASSED = Total_Global_Pass;
+
+    // TrigWind << TRIG_WINDOW_Size << "\t" << Total_Global_Pass << endl;
+    // cout << "TRIG_WINDOW_Size:Total_Global_Pass:: " << TRIG_WINDOW_Size << " : " << Total_Global_Pass << endl;
+
+    // }// end trigger window loop
+    TrigWind.close();
+                                         
+    //--------------------------------------------------
+    //    cFull_window_V->Print("test_V_mimic.pdf");
+    //-------------------------------------------------- 
+
+    ofstream weight_file;
+    //weight_file.open(("./weight_output/weight_"+setupfile).c_str());
+    if (argc == 3) {
+        weight_file.open(("./weight_output/weight_"+setupfile+".run"+run_no).c_str());
+    }
+    else if (argc >3 ){ // add the subdirectory for outputs
+        weight_file.open((outputdir+"/weight_output/weight_"+setupfile+".run"+run_no).c_str());
+    }
+    else {
+        weight_file.open(("./weight_output/weight_"+setupfile).c_str());
+    }
+
+
+    cout<<" end loop"<<endl;
+    // cout << "Total Events Thrown: " <<     settings1->NNU << endl;
+    cout << "Total Events Thrown: " << Events_Thrown << endl;
+    cout<<"Total_Global_Pass : "<<Total_Global_Pass<<endl;
+    cout<<"Total_Weight : "<<Total_Weight<<endl;
+    cout<<"Total_Probability : "<<Total_Probability<<endl;
+                             
+    if (settings1->INTERACTION_MODE==1) {
+        weight_file << "Total_Weight="<<Total_Weight<<endl;
+    }
+    else if (settings1->INTERACTION_MODE==0) {
+        weight_file << "Total_Probability="<<Total_Probability<<endl;
+    }
+
+    cout<<"weight bin values : ";
+    for (int i=0; i<count1->NBINS-1; i++) {
+        cout<<count1->eventsfound_binned[i]<<", ";
+        weight_file << count1->eventsfound_binned[i]<<" ";
+    }
+    cout<<count1->eventsfound_binned[count1->NBINS-1];
+    weight_file << count1->eventsfound_binned[count1->NBINS-1]<<"\n";
+    weight_file.close();
+    cout<<"\n\n";
+
+
+    // if using picknear_cylinder method
+    if (settings1->INTERACTION_MODE==1) {
+        double IceVolume;
+        IceVolume = PI * (settings1->POSNU_RADIUS) * (settings1->POSNU_RADIUS) * icemodel->IceThickness( detector->stations[0] );
+        cout << "Radius: " << settings1->POSNU_RADIUS << " [m]" << endl;
+        cout<<"IceVolume : "<<IceVolume<<endl;
+
+        double Veff_test_we; // effective volume water equivalent
+        double Veff_test; // effective volume ice
+
+        // error bar for weight
+        double error_plus = 0;
+        double error_minus = 0;
+        Counting::findErrorOnSumWeights( count1->eventsfound_binned, error_plus, error_minus );
+
+        /*       
+        Veff_test = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * Total_Weight / (double)(settings1->NNU);
+
+        // account all factors to error
+        error_plus = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * error_plus / (double)(settings1->NNU);
+        error_minus = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * error_minus / (double)(settings1->NNU);
+        */
+
+        Veff_test_we = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * Total_Weight / (double)(settings1->NNU);
+        Veff_test = IceVolume * 4. * PI * Total_Weight / (double)(settings1->NNU);
+        error_plus = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * error_plus / (double)(settings1->NNU);
+        error_minus = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * error_minus / (double)(settings1->NNU);
+
+        cout<<"test Veff(ice) : "<<Veff_test<<" m3sr, "<<Veff_test*1.E-9<<" km3sr"<<endl;
+        cout<<"test Veff(water eq.) : "<<Veff_test_we<<" m3sr, "<<Veff_test_we*1.E-9<<" km3sr"<<endl;
+        cout<<"And Veff(water eq.) error plus : "<<error_plus*1.E-9<<" and error minus : "<<error_minus*1.E-9<<endl;
+    }
+
+
+     // if using picknear_sphere method
+     //
+     else if (settings1->INTERACTION_MODE==0) {
+
+        double IceArea;
+        IceArea = PI * (settings1->POSNU_RADIUS) * (settings1->POSNU_RADIUS);
+        cout << endl;
+        cout<<"IceArea : "<< IceArea <<endl;
+
+        double Aeff;
+        Aeff = IceArea * Total_Probability / (double)(settings1->NNU);
+        cout << "Aeff : " << Aeff << " [m^2]" << endl;
+
+
+        // error bar for weight
+        double error_plus = 0;
+        double error_minus = 0;
+        Counting::findErrorOnSumWeights( count1->eventsfound_binned, error_plus, error_minus );
+
+        // account all factors to error
+        error_plus = IceArea * error_plus / (double)(settings1->NNU);
+        error_minus = IceArea * error_minus / (double)(settings1->NNU);
+
+        cout<<"And Aeff error plus : "<<error_plus<<" and error minus : "<<error_minus<<" [m^2]"<<endl;
+
+        // Aeff*sr
+        cout<<"and Aeff*sr values are"<<endl;
+        cout << "Aeff*sr : " << Aeff * 4.* PI << " [m^2sr]" <<", "<< Aeff * 4.* PI *1.e-6<<" [km^2sr]"<< endl;
+    }
+
+
+    //--------------------------------------------------
+    //   cout<<"Total NNU : "<<settings1->NNU<<", PickUnbiased passed NNU : "<<nnu_pass<<endl;
+    //-------------------------------------------------- 
+
+    // remove noisewaveform info if DATA_SAVE_MODE == 2
+    // remove noisewaveform info if DATA_SAVE_MODE is not 0
+    if (settings1->DATA_SAVE_MODE != 0) {
+        trigger->v_noise_timedomain.clear();
+        trigger->v_noise_timedomain_diode.clear();
+    }
+    if (settings1->DATA_SAVE_MODE == 2) {// in DATA_SAVE_MODE==2, remove noise spectrum before Rayleigh dist.
+        trigger->Vfft_noise_before.clear();
+    }
+
+    AraTree->Fill();  // fill tree for one entry
+    AraFile->Write();
+    // AraFile->Close();
+
+    efficiencies->summarize(); // summarize the results in an output file  
+
+    double freq[detector->GetFreqBin()], Filter[detector->GetFreqBin()];
+    double Filter_E[detector->GetFreqBin()];
+
+    for (int i=0; i<detector->GetFreqBin(); i++) {
+        freq[i] = detector->GetFreq(i);    // in Hz
+        Filter[i] = detector->GetFilterGain(i);    // in dB
+        Filter_E[i] = pow(10., (detector->GetFilterGain(i))/20.);
+    }
+
+    cout<<"max_dt : "<<max_dt<<endl;
+    cout<<"rmsdiode= "<<trigger->rmsdiode<<endl;
+
+    delete raysolver;
+    delete icemodel;
+    delete efficiencies;
+    delete ray;
+    delete detector;
+    delete settings1;
+    delete count1;
+    delete primary1;
+    delete trigger;
+    delete spectra;
+    delete sec1;
+    delete signal;
+
+    cout<<"outputdir= "<<outputdir<<endl;
+
+    // Please do not delete this test line
+    // Please leave 'test(); return 0;' as the last lines in 
+    // AraSim.cc before '} //end main'
+    // These test lines are used to verify that AraSim completed properly.
+
+    test();
+    return 0;   
+} //end main
+
+
+void test() {
+    cout << "test is " << 0 << "\n";
+}
diff --git a/.gitignore b/.gitignore
index 33c69fad..77fa84c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
 eventSimDict.C
 eventSimDict.h
 AraSim
+*.ipynb
\ No newline at end of file
diff --git a/AraSim.cc b/AraSim.cc
index 179c6dcf..2c8682d0 100644
--- a/AraSim.cc
+++ b/AraSim.cc
@@ -1,6 +1,6 @@
 // ROOT includes
 #include "TFile.h"
-#include "TRandom3.h" 
+#include "TRandom3.h"
 #include "TTree.h"
 
 // AraSim includes
@@ -42,7 +42,7 @@ void test();
 string outputdir="outputs";
 
 int main(int argc, char **argv) {   // read setup.txt file
-    
+
     Settings *settings1 = new Settings();
 
     cout<<"\n\tDefault values!"<<endl;
@@ -88,7 +88,7 @@ int main(int argc, char **argv) {   // read setup.txt file
         cerr<<"There are "<< settings_compatibility_error<<" errors from settings. Check error messages."<<endl;
         return -1;
     }
- 
+
     cout<<"\n\tNew values!"<<endl;
     cout<<"NNU : "<<settings1->NNU<<endl;
     cout<<"ICE_MODEL : "<<settings1->ICE_MODEL<<endl;
@@ -119,35 +119,35 @@ int main(int argc, char **argv) {   // read setup.txt file
         gRandom = test_randm3;
     } else {
         gRandom->SetSeed(settings1->SEED + atoi(run_no.c_str() ) );
-            
+
     }
     //cout<<"first random from TRandom3 : "<<test_randm3->Rndm()<<"\n";
     cout<<"first random : "<<gRandom->Rndm()<<"\n";
 
     // IceModel *icemodel=new IceModel(ICE_MODEL + NOFZ*10,CONSTANTICETHICKNESS * 1000 + CONSTANTCRUST * 100 + FIXEDELEVATION * 10 + 0,MOOREBAY);// creates Antarctica ice model
-    IceModel *icemodel=new IceModel(settings1->ICE_MODEL + settings1->NOFZ*10,settings1->CONSTANTICETHICKNESS * 1000 + settings1->CONSTANTCRUST * 100 + settings1->FIXEDELEVATION * 10 + 0,settings1->MOOREBAY);// creates Antarctica ice model
-    // IceModel inherits from EarthModel  
+    IceModel *icemodel=new IceModel(settings1->ICE_MODEL + settings1->NOFZ*10,settings1->CONSTANTICETHICKNESS * 1000 + settings1->CONSTANTCRUST * 100 + settings1->FIXEDELEVATION * 10 + 0,settings1->MOOREBAY, settings1->SYSTEMATICS_IceAtten);// creates Antarctica ice model
+    // IceModel inherits from EarthModel
 
     cout<<endl;
     cout<<"Surface at (log:0, lat:0) : "<<icemodel->Surface(0., 0.)<<endl;
     cout<<"SurfaceAboveGeoid at (log:0, lat:0) : "<<icemodel->SurfaceAboveGeoid(0., 0.)<<endl;
-    
+
     // Detector *detector=new Detector(settings1, icemodel); // builds antenna array, 0 for testbed
     Detector *detector=new Detector(settings1, icemodel, setupfile ); // builds antenna array, 0 for testbed
     cout<<"end calling detector"<<endl;
     // Detector *detector=new Detector(settings1->DETECTOR); // builds antenna array, 0 for testbed
 
-    Trigger *trigger=new Trigger(detector, settings1); // builds the trigger  
+    Trigger *trigger=new Trigger(detector, settings1); // builds the trigger
     // Efficiencies *efficiencies=new Efficiencies(detector->getnRx(),outputdir); // keeps track of efficiencies at each stage of the simulation
     Efficiencies *efficiencies=new Efficiencies(100,outputdir); // keeps track of efficiencies at each stage of the simulation
     cout<<"called Efficiencies"<<endl;
-    
+
     Spectra *spectra=new Spectra(settings1->EXPONENT); // gets library (or whatever) of neutrino spectra
     cout<<"called Spectra"<<endl;
 
     Ray *ray = new Ray(); // construct Ray class
     cout<<"called Ray"<<endl;
-    
+
 
     // test PickUnbiased in IceModel.
     Counting *count1 = new Counting();
@@ -160,7 +160,7 @@ int main(int argc, char **argv) {   // read setup.txt file
     //--------------------------------------------------
     //   Interaction *interaction1=new Interaction("nu",primary1,settings1,whichray,count1);
     //   cout<<"called Interaction1"<<endl;
-    //-------------------------------------------------- 
+    //--------------------------------------------------
 
     Event *event = new Event();
     cout<<"called Event"<<endl;
@@ -207,7 +207,7 @@ int main(int argc, char **argv) {   // read setup.txt file
     #ifdef ARA_UTIL_EXISTS
         UsefulIcrrStationEvent *theIcrrEvent =0;
         UsefulAtriStationEvent *theAtriEvent =0;
-    
+
 
         TTree *eventTree;
 
@@ -265,7 +265,7 @@ int main(int argc, char **argv) {   // read setup.txt file
 
     double max_dt = 0.; // max arrival time difference
 
-    int Total_Global_Pass = 0;  // total global trigger passed number 
+    int Total_Global_Pass = 0;  // total global trigger passed number
     double Total_Weight = 0.;
     double Total_Probability = 0.;
 
@@ -311,13 +311,13 @@ int main(int argc, char **argv) {   // read setup.txt file
 
     ofstream TrigWind;
     TrigWind.open("outputs/TrigWindowStudy.txt");
-        
-        
+
+
     // for (int iTrigWind = 10; iTrigWind < 201; iTrigWind = iTrigWind+10){
-        
+
     //  double TRIG_WINDOW_Size = double (iTrigWind * 1.0E-9);
     //  settings1->TRIG_WINDOW = TRIG_WINDOW_Size;
-                
+
     Total_Global_Pass = 0;
     cout<<"begin looping events!!"<<endl;
 
@@ -348,7 +348,7 @@ int main(int argc, char **argv) {   // read setup.txt file
 
 
 
-                
+
     // check if settings have to compatibility problems
     // if there's any, stop AraSim
     settings_compatibility_error = settings1->CheckCompatibilitiesDetector(detector);
@@ -356,7 +356,7 @@ int main(int argc, char **argv) {   // read setup.txt file
         cerr<<"There are "<< settings_compatibility_error<<" errors from settings after Detector class instance is initialized. Check error messages."<<endl;
         return -1;
     }
-        
+
     #ifndef ARA_UTIL_EXISTS
         if (settings1->DETECTOR == 3 && settings1->READGEOM == 1){
             cerr << "ERROR::InstalledStation geometry not available without AraRoot installation!" << endl;
@@ -368,7 +368,7 @@ int main(int argc, char **argv) {   // read setup.txt file
     // test autoflush
     // AraTree2->SetAutoFlush(0);
 
-    // reset accumulative trig search bin info 
+    // reset accumulative trig search bin info
     settings1->ACCUM_TRIG_SEARCH_BINS_STATION0 = 0.;
 
     int nuLimit =0;
@@ -381,13 +381,13 @@ int main(int argc, char **argv) {   // read setup.txt file
     else {
         nuLimit = settings1->NNU;
     }
-    // cout << "nuLimit: " << nuLimit << endl; 
+    // cout << "nuLimit: " << nuLimit << endl;
     int inu = 0;
     int Events_Thrown = 0;
     int Events_Passed = 0;
     // for (int inu=0;inu<settings1->NNU;inu++) { // loop over neutrinos
     while (inu < nuLimit){
-        // cout << "inu: " << inu << endl; 
+        // cout << "inu: " << inu << endl;
         check_station_DC = 0;
         check_station_DC = 0;
         if ( settings1->DEBUG_MODE_ON==0 ) {
@@ -399,9 +399,9 @@ int main(int argc, char **argv) {   // read setup.txt file
         // event = new Event ( settings1, spectra, primary1, icemodel, detector, signal, sec1 );
         event = new Event ( settings1, spectra, primary1, icemodel, detector, signal, sec1, Events_Thrown );
         event->inu_passed = -1;
-                
+
         report = new Report(detector, settings1);
-                        
+
         #ifdef ARA_UTIL_EXISTS
             theIcrrEvent = new UsefulIcrrStationEvent();
             theAtriEvent = new UsefulAtriStationEvent();
@@ -429,7 +429,7 @@ int main(int argc, char **argv) {   // read setup.txt file
             // cout<<"nu_flavor : "<<event->nuflavor<<endl;
             // cout<<"event->Nu_Interaction[0].vmmhz1m[0] : "<<event->Nu_Interaction[0].vmmhz1m[0]<<endl;
             // cout<<"pickposnu : "<<event->Nu_Interaction[0].pickposnu<<endl;
-            //-------------------------------------------------- 
+            //--------------------------------------------------
 
             // connect Interaction class (nu interaction with ice) and Detector class (detector properties and layout)
             // save signal, noise at each antennas to Report class
@@ -466,9 +466,9 @@ int main(int argc, char **argv) {   // read setup.txt file
                     }
                     weight = event->Nu_Interaction[0].weight;
                 }
-                // cout << "weight: " << weight <<endl;    
+                // cout << "weight: " << weight <<endl;
             #endif
-                     
+
             report->ClearUselessfromConnect(detector, settings1, trigger);
             for(int i=0;i<event->Nu_Interaction.size(); i++)
                 event->Nu_Interaction[i].clear_useless(settings1);
@@ -496,24 +496,24 @@ int main(int argc, char **argv) {   // read setup.txt file
                             { theIcrrEvent->numRFChans = 14; }
                         else if (settings1->DETECTOR == 4 && settings1->DETECTOR_STATION == 0)
                             { theIcrrEvent->numRFChans = 14; }
-                        else { 
-                            theAtriEvent->fNumChannels = 20; 
-                            theIcrrEvent->numRFChans = 16; 
+                        else {
+                            theAtriEvent->fNumChannels = 20;
+                            theIcrrEvent->numRFChans = 16;
                         }
                     }
                 #endif
-                     
+
                 if (max_dt < report->stations[i].max_arrival_time - report->stations[i].min_arrival_time)
                     max_dt = report->stations[i].max_arrival_time - report->stations[i].min_arrival_time;
                 // check the total global trigger passed
                 if (report->stations[i].Global_Pass) {
                     cout<<"\nGlobal_Pass : "<<report->stations[i].Global_Pass<<" evt : "<<inu<<" added weight : "<<event->Nu_Interaction[0].weight<<endl;
                     if ( check_station_DC == 0) { // count trigger pass only once per event
-                             
+
                         Total_Global_Pass ++;
                         Total_Weight += event->Nu_Interaction[0].weight;
                         Total_Probability += event->Nu_Interaction[0].probability;
-                             
+
                         // test increment weight
                         if (settings1->INTERACTION_MODE==1) {
                             count1->incrementEventsFound( event->Nu_Interaction[0].weight, event );
@@ -526,10 +526,10 @@ int main(int argc, char **argv) {   // read setup.txt file
                         }
                         else if (settings1->INTERACTION_MODE==4) {
                             count1->incrementEventsFound( event->Nu_Interaction[0].weight, event );
-                        }    
+                        }
                     }
                     check_station_DC++;
-                    event->inu_passed = Events_Passed; 
+                    event->inu_passed = Events_Passed;
                 }
             }
 
@@ -563,7 +563,7 @@ int main(int argc, char **argv) {   // read setup.txt file
 
 
         // test FILL_TREE_MODE
-        if (settings1->FILL_TREE_MODE==0) { // fill event event  
+        if (settings1->FILL_TREE_MODE==0) { // fill event event
             AraTree2->Fill();   //fill interaction every events
             #ifdef ARA_UTIL_EXISTS
                 // for 1, save all events whether passed trigger or not
@@ -580,7 +580,7 @@ int main(int argc, char **argv) {   // read setup.txt file
                 }
             #endif
         }
-        else if (settings1->FILL_TREE_MODE==1) { // fill only usable posnu event 
+        else if (settings1->FILL_TREE_MODE==1) { // fill only usable posnu event
             if (event->Nu_Interaction[0].pickposnu>0) {
                 AraTree2->Fill();   //fill interaction every events
                 #ifdef ARA_UTIL_EXISTS
@@ -599,7 +599,7 @@ int main(int argc, char **argv) {   // read setup.txt file
                 #endif
             }
         }
-        else if (settings1->FILL_TREE_MODE==2) { // fill only triggered event    
+        else if (settings1->FILL_TREE_MODE==2) { // fill only triggered event
             if (check_station_DC>0) {
                 AraTree2->Fill();   //fill interaction every events
                 #ifdef ARA_UTIL_EXISTS
@@ -633,7 +633,7 @@ int main(int argc, char **argv) {   // read setup.txt file
             Events_Passed++;
         }
         Events_Thrown++;
-             
+
 
         //theEvent = NULL;
 
@@ -666,10 +666,10 @@ int main(int argc, char **argv) {   // read setup.txt file
 
     // }// end trigger window loop
     TrigWind.close();
-                                         
+
     //--------------------------------------------------
     //    cFull_window_V->Print("test_V_mimic.pdf");
-    //-------------------------------------------------- 
+    //--------------------------------------------------
 
     ofstream weight_file;
     //weight_file.open(("./weight_output/weight_"+setupfile).c_str());
@@ -690,7 +690,7 @@ int main(int argc, char **argv) {   // read setup.txt file
     cout<<"Total_Global_Pass : "<<Total_Global_Pass<<endl;
     cout<<"Total_Weight : "<<Total_Weight<<endl;
     cout<<"Total_Probability : "<<Total_Probability<<endl;
-                             
+
     if (settings1->INTERACTION_MODE==1) {
         weight_file << "Total_Weight="<<Total_Weight<<endl;
     }
@@ -724,7 +724,7 @@ int main(int argc, char **argv) {   // read setup.txt file
         double error_minus = 0;
         Counting::findErrorOnSumWeights( count1->eventsfound_binned, error_plus, error_minus );
 
-        /*       
+        /*
         Veff_test = IceVolume * 4. * PI * signal->RHOICE / signal->RHOH20 * Total_Weight / (double)(settings1->NNU);
 
         // account all factors to error
@@ -776,7 +776,7 @@ int main(int argc, char **argv) {   // read setup.txt file
 
     //--------------------------------------------------
     //   cout<<"Total NNU : "<<settings1->NNU<<", PickUnbiased passed NNU : "<<nnu_pass<<endl;
-    //-------------------------------------------------- 
+    //--------------------------------------------------
 
     // remove noisewaveform info if DATA_SAVE_MODE == 2
     // remove noisewaveform info if DATA_SAVE_MODE is not 0
@@ -792,7 +792,7 @@ int main(int argc, char **argv) {   // read setup.txt file
     AraFile->Write();
     // AraFile->Close();
 
-    efficiencies->summarize(); // summarize the results in an output file  
+    efficiencies->summarize(); // summarize the results in an output file
 
     double freq[detector->GetFreqBin()], Filter[detector->GetFreqBin()];
     double Filter_E[detector->GetFreqBin()];
@@ -822,12 +822,12 @@ int main(int argc, char **argv) {   // read setup.txt file
     cout<<"outputdir= "<<outputdir<<endl;
 
     // Please do not delete this test line
-    // Please leave 'test(); return 0;' as the last lines in 
+    // Please leave 'test(); return 0;' as the last lines in
     // AraSim.cc before '} //end main'
     // These test lines are used to verify that AraSim completed properly.
 
     test();
-    return 0;   
+    return 0;
 } //end main
 
 
diff --git a/Detector.cc b/Detector.cc
index 5d9d6ade..c00ad821 100644
--- a/Detector.cc
+++ b/Detector.cc
@@ -1966,7 +1966,7 @@ Detector::Detector(Settings *settings1, IceModel *icesurface, string setupfile)
 
         
         //        cout<<"total station_count : "<<station_count<<endl;
-        if (station_count != (int)params.number_of_stations) cout<<"\n\tError, station number not match !"<<endl;
+        //if (station_count != (int)params.number_of_stations) cout<<"\n\tError, station number not match !"<<endl;
         
         //
         // set antenna values from parameters
@@ -2289,6 +2289,23 @@ inline void Detector::ReadVgain(string filename) {
 }// end ReadVgain
 
 inline void Detector::ReadVgain(string filename, Settings *settings1) {
+
+   // Read 600MHz low-pass filter for uncertainty estimate
+   ifstream in;
+   in.open("filter7pole600MHz.txt", std::ifstream::in);
+   double filterValue[60];
+   double filterFreq[60];
+   double tempFilter, tempFilterFreq;
+
+   if(in.good()){
+      for(int i=0;i<60;i++){
+         in >> tempFilterFreq >> tempFilter;
+         filterValue[i] = tempFilter;
+         filterFreq[i] = tempFilterFreq;
+      }
+   }
+   in.close();
+
     ifstream NecOut( filename.c_str() );
     const int N = freq_step;
     double Transm[N];
@@ -2309,7 +2326,11 @@ inline void Detector::ReadVgain(string filename, Settings *settings1) {
                     for (int j=0; j<ang_step; j++) {
                         getline (NecOut, line); //read data line
                         //Vgain[i][j] = atof( line.substr( 18 ).c_str() );  // read gain (not dB)
-                        Vgain[i][j] = Transm[i] * atof( line.substr( 20, 33 ).c_str() );  // read gain (not dB)
+                        if (settings1->USE_SIGNAL_CHAIN_LOWER_BOUND == 0){ //default
+                           Vgain[i][j] = Transm[i] * atof( line.substr( 20, 33 ).c_str() );  // read gain (not dB)
+                        } else { //systematic error estimate: 600MHz low-pass filter + SC effi. lower bound
+                           Vgain[i][j] = Transm[i] * atof( line.substr( 20, 33 ).c_str() ) * filterValue[i] * settings1->SC_EFFICIENCY_ERROR_V;  // read gain (not dB)
+                        }
                         Vphase[i][j] = atof( line.substr( 34 ).c_str() );  // read gain (not dB)
                                                 
                         //cout<<"VGain : "<<Vgain[i][j]<<", VPhase : "<<Vphase[i][j]<<endl;
@@ -2349,6 +2370,24 @@ inline void Detector::ReadVgain(string filename, Settings *settings1) {
 
 
 inline void Detector::ReadVgainTop(string filename, Settings *settings1) {
+
+   // Read 600MHz low-pass filter for uncertainty estimate
+   ifstream in;
+   in.open("filter7pole600MHz.txt", std::ifstream::in);
+   double filterValue[60];
+   double filterFreq[60];
+   double tempFilter, tempFilterFreq;
+
+   if(in.good()){
+      for(int i=0;i<60;i++){
+         in >> tempFilterFreq >> tempFilter;
+         filterValue[i] = tempFilter;
+         filterFreq[i] = tempFilterFreq;
+      }
+   }
+   in.close();
+
+
     ifstream NecOut( filename.c_str() );
     const int N = freq_step;
 
@@ -2364,13 +2403,18 @@ inline void Detector::ReadVgainTop(string filename, Settings *settings1) {
                     //                    cout<<"freq["<<i<<"] = "<<Freq[i]<<" MHz"<<endl;
                     getline (NecOut, line); //read SWR
 		    Transm[i] = atof( line.substr(5, 11).c_str() );
-		      cerr << "Vpol Transm: " << Transm[i] << endl;
+		      // cerr << "Vpol Transm: " << Transm[i] << endl;
 
                     getline (NecOut, line); //read names
 
                     for (int j=0; j<ang_step; j++) {
                         getline (NecOut, line); //read data line
+                        if(settings1->USE_SIGNAL_CHAIN_LOWER_BOUND == 0){
                         VgainTop[i][j] = Transm[i]*atof( line.substr( 20, 33 ).c_str() );
+                        } else { //systematic error estimate: 600MHz low-pass filter + SC effi. lower bound
+                        VgainTop[i][j] = Transm[i] * atof( line.substr( 20, 33 ).c_str() ) * filterValue[i] * settings1->SC_EFFICIENCY_ERROR_V;  // read gain (not dB)
+                        }
+ 
                         VphaseTop[i][j] = atof( line.substr( 34 ).c_str() );    // + 180.0/TMath::Pi()*TMath::ATan(-Freq[i]/500.0);  // read gain (not dB)
                                                 
                         //cout<<"VGain : "<<Vgain[i][j]<<", VPhase : "<<Vphase[i][j]<<endl;
@@ -2412,6 +2456,7 @@ inline void Detector::ReadVgainTop(string filename, Settings *settings1) {
 
 
 inline void Detector::ReadHgain(string filename) {
+
   ifstream NecOut( filename.c_str() );
     
     string line;
@@ -2451,6 +2496,24 @@ inline void Detector::ReadHgain(string filename) {
 
 inline void Detector::ReadHgain(string filename, Settings *settings1) {
 
+   // Read 600MHz low-pass filter for uncertainty estimate
+   ifstream in;
+   in.open("filter7pole600MHz.txt", std::ifstream::in);
+   double filterValue[60];
+   double filterFreq[60];
+   double tempFilter, tempFilterFreq;
+
+   if(in.good()){
+      for(int i=0;i<60;i++){
+         in >> tempFilterFreq >> tempFilter;
+         filterValue[i] = tempFilter;
+         //cout<<"filterValue: "<<filterValue[i]<<endl;
+         filterFreq[i] = tempFilterFreq;
+      }
+   }
+   in.close();
+
+
     ifstream NecOut( filename.c_str() );    
     string line;
     
@@ -2473,7 +2536,13 @@ inline void Detector::ReadHgain(string filename, Settings *settings1) {
                         getline (NecOut, line); //read data line
                         //Hgain[i][j] = atof( line.substr( 20 ).c_str() );  // read gain (not dB)
                         //Hgain[i][j] = atof( line.substr( 18, 25 ).c_str() );  // read gain (not dB)
+                        if(settings1->USE_SIGNAL_CHAIN_LOWER_BOUND == 0){
                         Hgain[i][j] = Transm[i]*atof( line.substr( 20, 33 ).c_str() );  // read gain (not dB)
+                        } else { //systematic error estimate: 600MHz low-pass filter + SC effi. lower bound
+                        Hgain[i][j] = Transm[i] * atof( line.substr( 20, 33 ).c_str() ) * filterValue[i] * settings1->SC_EFFICIENCY_ERROR_H;  // read gain (not dB)
+                        //cout<<"SC effi low H: "<<settings1->SC_EFFICIENCY_ERROR_H<<endl;
+                        }
+ 
                         Hphase[i][j] = atof( line.substr( 34 ).c_str() );  // read gain (not dB)
 
                         //cout<<"HGain : "<<Hgain[i][j]<<", HPhase : "<<Hphase[i][j]<<endl;
@@ -4204,10 +4273,10 @@ cout<<"In ReadNoiseFigure"<<endl;
 	        iss >> sub;
 		yNF_tmp.push_back( atof(sub.c_str()) );
 	    }
-	    cout << "freq: " << yNF_tmp[0];
+	    // cout << "freq: " << yNF_tmp[0];
 	    all_chNF.push_back( yNF_tmp );
 	    yNF_tmp.clear();
-	    cout << "   ch1: " << all_chNF[N][1] << endl;
+	    // cout << "   ch1: " << all_chNF[N][1] << endl;
             
             N++;
             
@@ -4422,17 +4491,17 @@ inline void Detector::ReadElectChain(string filename, Settings *settings1) {
             N++;
 
             xfreq_tmp.push_back( atof( line.substr(0, line.find_first_of(",")).c_str() ) );
-            cout<<"freq : "<<xfreq_tmp[N]<<"\t";
+            // cout<<"freq : "<<xfreq_tmp[N]<<"\t";
 
             line2 = line.substr( line.find_first_of(",")+1);
 
             ygain_tmp.push_back( atof( line2.substr(0, line2.find_first_of(",")).c_str() ) );
-            cout<<"gain : "<<ygain_tmp[N]<<"\t";
+            // cout<<"gain : "<<ygain_tmp[N]<<"\t";
 
             line3 = line2.substr( line2.find_first_of(",")+1);
 
             phase_tmp.push_back( atof( line3.substr(0).c_str() ) );
-            cout<<"phase : "<<phase_tmp[N]<<" N : "<<N<<endl;
+            // cout<<"phase : "<<phase_tmp[N]<<" N : "<<N<<endl;
 
             /*
             xfreq_tmp.push_back( atof( line.substr(0, 10).c_str() ) );
diff --git a/IceModel.cc b/IceModel.cc
index 309cc012..66911321 100644
--- a/IceModel.cc
+++ b/IceModel.cc
@@ -24,13 +24,13 @@ using namespace std;
 
 //class Interaction;
 
-
-
+// int SYSTEMAT_IceAtten;
+//
 //Parameters of the BEDMAP ice model. (See http://www.antarctica.ac.uk/aedc/bedmap/download/)
 int nCols_ice=1200; //number of columns in data, set by header file (should be 1200)
 int nRows_ice=1000; //number of rows in data, set by header file (should be 1000)
 int cellSize=5000; //in meters, set by header file (should be 5000) - same for both files
-int xLowerLeft_ice=-3000000; 
+int xLowerLeft_ice=-3000000;
 int yLowerLeft_ice=-2500000;
 int nCols_ground=1068;
 int nRows_ground=869;
@@ -41,7 +41,6 @@ int nRows_water=1000;
 int xLowerLeft_water=-3000000;
 int yLowerLeft_water=-2500000;
 int NODATA=-9999;
-
 //Variables for conversion between BEDMAP polar stereographic coordinates and lat/lon.  Conversion equations from ftp://164.214.2.65/pub/gig/tm8358.2/TM8358_2.pdf
 const double scale_factor=0.97276901289;  //scale factor at pole corresponding to 71 deg S latitude of true scale (used in BEDMAP)
 const double ellipsoid_inv_f = 298.257223563; //of Earth
@@ -61,9 +60,9 @@ IceModel::IceModel() {
 }
 */
 
-IceModel::IceModel(int model,int earth_model,int moorebay) : EarthModel(earth_model),mooreBayFlag(moorebay) {
+IceModel::IceModel(int model,int earth_model,int moorebay, int SYSTEMATICS_IceAtten) : EarthModel(earth_model),mooreBayFlag(moorebay) {
 
-  setUpIceModel(model);
+  setUpIceModel(model,SYSTEMATICS_IceAtten);
 
  }
 
@@ -73,8 +72,8 @@ IceModel::~IceModel () {
 }
 
 
-void IceModel::setUpIceModel(int model) {
-  
+void IceModel::setUpIceModel(int model, int SYSTEMATICS_IceAttenuation) {
+
   DEPTH_DEPENDENT_N = (int) (model / 10);
   model -= DEPTH_DEPENDENT_N * 10;
   ice_model=model;
@@ -96,21 +95,21 @@ void IceModel::setUpIceModel(int model) {
       cerr << "Failed to open icesheet_attenlength_up.txt" << endl;
       exit(1);
     }
-  
+
   i=0;
   while(sheetup>>d_sheetup[i]>>l_sheetup[i])
     {
       i++;
     }
   sheetup.close();
-   
+
   ifstream shelfup("data/iceshelf_attenlength_up.txt");
   if(shelfup.fail())
     {
       cerr << "Failed to open iceshelf_attenlength_up.txt" << endl;
       exit(1);
     }
-  
+
   i=0;
   while(shelfup>>d_shelfup[i]>>l_shelfup[i])
     {
@@ -129,7 +128,7 @@ void IceModel::setUpIceModel(int model) {
       i++;
     }
   westlandup.close();
-   
+
   //read in attenuation length for downgoing signals
   ifstream sheetdown("data/icesheet_attenlength_down.txt");
   if(sheetdown.fail())
@@ -137,7 +136,7 @@ void IceModel::setUpIceModel(int model) {
       cerr << "Failed to open icesheet_attenlength_down.txt" << endl;
       exit(1);
     }
-  
+
   i=0;
   while(sheetdown>>d_sheetdown[i]>>l_sheetdown[i])
     {
@@ -152,14 +151,14 @@ void IceModel::setUpIceModel(int model) {
       cerr << "Failed to open iceshelf_attenlength_down.txt" << endl;
       exit(1);
     }
-  
+
   i=0;
   while(shelfdown>>d_shelfdown[i]>>l_shelfdown[i])
     {
       i++;
     }
   shelfdown.close();
-   
+
   ifstream westlanddown("data/westland_attenlength_down.txt");
   if(westlanddown.fail())
     {cerr << "Failed to open westland_attenlength_down.txt";
@@ -189,14 +188,14 @@ void IceModel::setUpIceModel(int model) {
 
 if ( file.is_open() ) {
     while (file.good() ) {
-        
+
         if ( first_time == 1 ) {
             for (int sl=0; sl<skipline; sl++) {
                 getline (file, line);
             }
             first_time = 0;
         }
-                
+
 
         getline (file, line);
 
@@ -223,24 +222,103 @@ if ( file.is_open() ) {
 
     // done reading ARA ice attenuation info
     */
+  //The following hardcoded numbers correspond to a model derived by Eugene Hong, based on ice attenuation measurements (c.f. TestBed paper). This is the default mode usedf by AraSim.
+ //More details can be found on Eugene's Thesis: http://radiorm.physics.ohio-state.edu/elog/Write-Ups/170504_105713/Thesis_-_Eugene_Hong.pdf, p. 54 and 132.
+//SYSTEMAT_IceAtten = settings1->SYSTEMATICS_IceAtten;
+ // int SYSTEMAT_IceAtten = 0;
+ // NB: the difference in the three models are the *depths* not the *length*s
+ // NB: that's a somewhat non-traditional way of doing it, but should work
+ ARA_IceAtten_bin = 53;
+ if(SYSTEMATICS_IceAttenuation == 0){
+   double ARA_IceAtten_Depth_central[53] =
+      { 72.7412,   76.5697,    80.3982,    91.8836,    95.7121,    107.198,
+        118.683,    133.997,    153.139,    179.939,    206.738,    245.023,
+        298.622,    356.049,    405.819,    470.904,    516.845,    566.616,
+        616.386,    669.985,    727.412,    784.839,    838.438,    899.694,
+        949.464,    1003.06,    1060.49,    1121.75,    1179.17,    1236.6,
+        1297.86,    1347.63,    1405.05,    1466.31,    1516.08,    1565.85,
+        1611.79,    1657.73,    1699.85,    1745.79,    1791.73,    1833.84,
+        1883.61,    1929.56,    1990.81,    2052.07,    2109.49,    2170.75,
+        2232.01,    2304.75,    2362.17,    2431.09,    2496.17 };
+   double ARA_IceAtten_Length_central[53] =
+      { 1994.67,   1952,    1896,    1842.67,    1797.33,    1733.33,
+        1680,      1632,    1586.67, 1552,       1522.67,    1501.33,
+        1474.67,   1458.67, 1437.33, 1416,       1392,       1365.33,
+        1344,      1312,    1274.67, 1242.67,    1205.33,    1168,
+        1128,    1090.67,    1048,    1008,      965.333,    920,
+        874.667,    834.667,    797.333,    752,    714.667, 677.333,
+        648,    616,    589.333,    557.333,    530.667,    506.667,
+        477.333,    453.333,    418.667,    389.333,    362.667,
+        333.333,    309.333,    285.333,    264,    242.667,    221.333 };
+
+   std::copy(ARA_IceAtten_Depth_central,ARA_IceAtten_Depth_central+ARA_IceAtten_bin,ARA_IceAtten_Depth);
+   std::copy(ARA_IceAtten_Length_central,ARA_IceAtten_Length_central+ARA_IceAtten_bin,ARA_IceAtten_Length);
 
-  //
-  double ARA_IceAtten_Depth_tmp[53] = { 72.7412,   76.5697,    80.3982,    91.8836,    95.7121,    107.198,    118.683,    133.997,    153.139,    179.939,    206.738,    245.023,    298.622,    356.049,    405.819,    470.904,    516.845,    566.616,    616.386,    669.985,    727.412,    784.839,    838.438,    899.694,    949.464,    1003.06,    1060.49,    1121.75,    1179.17,    1236.6,    1297.86,    1347.63,    1405.05,    1466.31,    1516.08,    1565.85,    1611.79,    1657.73,    1699.85,    1745.79,    1791.73,    1833.84,    1883.61,    1929.56,    1990.81,    2052.07,    2109.49,    2170.75,    2232.01,    2304.75,    2362.17,    2431.09,    2496.17 };
-
-  double ARA_IceAtten_Length_tmp[53] = { 1994.67,   1952,    1896,    1842.67,    1797.33,    1733.33,    1680,    1632,    1586.67,    1552,    1522.67,    1501.33,    1474.67,    1458.67,    1437.33,    1416,    1392,    1365.33,    1344,    1312,    1274.67,    1242.67,    1205.33,    1168,    1128,    1090.67,    1048,    1008,    965.333,    920,    874.667,    834.667,    797.333,    752,    714.667,    677.333,    648,    616,    589.333,    557.333,    530.667,    506.667,    477.333,    453.333,    418.667,    389.333,    362.667,    333.333,    309.333,    285.333,    264,    242.667,    221.333 };
+}
 
-  ARA_IceAtten_bin = 53;
-  for (int bin=0; bin<ARA_IceAtten_bin; bin++) {
+ //Upper bound
+ //if upper bound, then
+ if(SYSTEMATICS_IceAttenuation == 1){
+   double ARA_IceAtten_Depth_up[53] =
+     { 171.  ,  189.  ,  258.44,  358.67,  455.76,  572.28,  635.86,
+       687.97,  746.55,  795.13,  839.62,  871.98,  898.61,  914.15,
+       934.88,  960.2 ,  991.4 , 1025.34, 1049.71, 1086.29, 1125.33,
+       1157.33, 1194.67, 1232.  , 1272.  , 1310.88, 1360.67, 1411.97,
+       1464.5 , 1512.58, 1561.93, 1603.87, 1640.  , 1693.15, 1739.18,
+       1792.38, 1829.23, 1858.77, 1885.91, 1937.53, 1980.5 , 2016.73,
+       2061.24, 2105.99, 2170.81, 2242.16, 2299.54, 2358.97, 2405.13,
+       2450.  , 2450.  , 2450.  , 2450. };
+
+    double ARA_IceAtten_Length_up[53] =
+       { 1994.67 , 1952.   , 1896.   , 1842.67 , 1797.33 , 1733.33 ,
+         1680.   , 1632.   , 1586.67 , 1552.   , 1522.67 , 1501.33 ,
+         1474.67 , 1458.67 , 1437.33 , 1416.   , 1392.   , 1365.33 ,
+         1344.   , 1312.   , 1274.67 , 1242.67 , 1205.33 , 1168.   ,
+         1128.   , 1090.67 , 1048.   , 1008.   ,  965.333,  920.   ,
+         874.667,  834.667,  797.333,  752.   ,  714.667,  677.333,
+         648.   ,  616.   ,  589.333,  557.333,  530.667,  506.667,
+         477.333,  453.333,  418.667,  389.333,  362.667,  333.333,
+         309.333,  285.333,  264.   ,  242.667,  221.333 };
+
+    std::copy(ARA_IceAtten_Depth_up, ARA_IceAtten_Depth_up+ARA_IceAtten_bin, ARA_IceAtten_Depth);
+    std::copy(ARA_IceAtten_Length_up, ARA_IceAtten_Length_up+ARA_IceAtten_bin, ARA_IceAtten_Length);
 
-      ARA_IceAtten_Depth[bin] = ARA_IceAtten_Depth_tmp[bin];
-      ARA_IceAtten_Length[bin] = ARA_IceAtten_Length_tmp[bin];
   }
 
+   //Lower bound
+   //if lower bound, then
+  if(SYSTEMATICS_IceAttenuation == 2){
+     double ARA_IceAtten_Depth_low[53] =
+     { 79.9 ,   81.78,   85.3 ,   87.97,   91.87,   97.73,  101.95,
+       109.4 ,  123.  ,  132.93,  141.24,  146.53,  153.01,  156.89,
+       168.5 ,  184.5 ,  202.5 ,  245.45,  281.28,  362.2 ,  471.68,
+       543.39,  616.38,  690.4 ,  774.4 ,  844.08,  915.73,  978.51,
+       1040.76, 1110.94, 1179.05, 1236.19, 1291.15, 1359.48, 1417.41,
+       1473.23, 1517.01, 1557.5 , 1591.21, 1649.39, 1697.74, 1740.59,
+       1792.54, 1829.06, 1892.58, 1959.24, 2017.25, 2082.31, 2137.69,
+       2194.45, 2245.24, 2302.73, 2369.08};
+
+      double ARA_IceAtten_Length_low[53] =
+       { 1994.67 , 1952.   , 1896.   , 1842.67 , 1797.33 , 1733.33 ,
+         1680.   , 1632.   , 1586.67 , 1552.   , 1522.67 , 1501.33 ,
+         1474.67 , 1458.67 , 1437.33 , 1416.   , 1392.   , 1365.33 ,
+         1344.   , 1312.   , 1274.67 , 1242.67 , 1205.33 , 1168.   ,
+         1128.   , 1090.67 , 1048.   , 1008.   ,  965.333,  920.   ,
+         874.667,  834.667,  797.333,  752.   ,  714.667,  677.333,
+         648.   ,  616.   ,  589.333,  557.333,  530.667,  506.667,
+         477.333,  453.333,  418.667,  389.333,  362.667,  333.333,
+         309.333,  285.333,  264.   ,  242.667,  221.333};
+
+      std::copy(ARA_IceAtten_Depth_low, ARA_IceAtten_Depth_low+ARA_IceAtten_bin, ARA_IceAtten_Depth);
+      std::copy(ARA_IceAtten_Length_low,ARA_IceAtten_Length_low+ARA_IceAtten_bin, ARA_IceAtten_Length);
 
- 
-}
+  }
 
+   for (int bin=0; bin<ARA_IceAtten_bin; bin++) {
+     //printf("bin:%i, ARA_IceAtten_Depth:%f, ARA_IceAtten_Length_tmp:%f \n", bin,ARA_IceAtten_Depth[bin],ARA_IceAtten_Length[bin]);
+   }
 
+}
 
 // read depth in positive value and return attenuation length (m) at the depth
 double IceModel::GetARAIceAttenuLength(double depth) {
@@ -278,10 +356,10 @@ Position IceModel::PickBalloonPosition() const {
 
 //--------------------------------------------------
 // int IceModel::PickUnbiased(int inu, Interaction *interaction1, IceModel *antarctica) {
-//     
-// 
+//
+//
 //   interaction1->PickAnyDirection(); // first pick the neutrino direction
-// 
+//
 //   double mincos=cos(COASTLINE*RADDEG);
 //   double maxcos=cos(0.);
 //   double minphi=0.;
@@ -289,14 +367,14 @@ Position IceModel::PickBalloonPosition() const {
 //   double thisphi,thiscos,thissin;
 //   double theta=0.;
 //   double phi=0.;
-// 
-//   int ilon,ilat;    
+//
+//   int ilon,ilat;
 //   int e_coord,n_coord;
 //   double vol_thisbin=0.;
 //   double lon=0.;
 //   double lat=0.;
-//   
-//  
+//
+//
 //     thisphi=gRandom->Rndm()*(maxphi-minphi)+minphi;
 //     thiscos=gRandom->Rndm()*(maxcos-mincos)+mincos;
 //     thissin=sqrt(1.-thiscos*thiscos);
@@ -312,7 +390,7 @@ Position IceModel::PickBalloonPosition() const {
 //     interaction1->wheredoesitenterice_err=0;
 //     interaction1->toohigh=0;
 //     interaction1->toolow=0;
-// 
+//
 //     thisr_in.SetXYZ(R_EARTH*thissin*cos(thisphi),R_EARTH*thissin*sin(thisphi),R_EARTH*thiscos);
 //     if (thisr_in.Dot(interaction1->nnu)>0)
 //       interaction1->nnu=-1.*interaction1->nnu;
@@ -320,123 +398,123 @@ Position IceModel::PickBalloonPosition() const {
 //     //cout << "lat, coastline, cos are " << thisr_in.Lat() << " " << COASTLINE << " " << cos(interaction1->nnu.Theta()) << "\n";
 //     if (thisr_in.Lat()>COASTLINE && cos(interaction1->nnu.Theta())<0) {
 //       interaction1->noway=1;
-// 
+//
 //       interaction1->pickunbiased=0;
 //       return 0; // there is no way it's going through the ice
 //     }
-// 
+//
 //     int count1=0;
 //     int count2=0;
-// 
-//    
+//
+//
 //     if (Ray::WhereDoesItLeave(0,thisr_in,interaction1->nnu,antarctica,thisnuexitearth)) { // where does it leave Earth
 //       // really want to find where it leaves ice
 //       int err;
 //       // Does it leave in an ice bin
 //       if (IceThickness(thisnuexitearth) && thisnuexitearth.Lat()<COASTLINE) { // if this is an ice bin in the Antarctic
-// 	//cout << "inu is " << inu << " it's in ice.\n";
-// 	//cout << "this is an ice bin.\n";
-// 	thisnuexitice=thisnuexitearth;
-// 	thisr_exitice=thisnuexitearth;
-// 	if (thisnuexitice.Mag()>Surface(thisnuexitice)) { // if the exit point is above the surface
-// 	  if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>5.E3) { 
-// 	    WhereDoesItExitIce(inu,thisnuexitearth,interaction1->nnu,5.E3, // then back up and find it more precisely
-// 			       thisr_exitice);
-// 	    thisnuexitice=(5000.)*interaction1->nnu;
-// 	    thisnuexitice+=thisr_exitice;
-// 	    count1++;
-// 	  }
-// 	  if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>5.E2) {
-// 	    
-// 	    WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E2, // then back up and find it more precisely
-// 			       thisr_exitice);
-// 	    thisnuexitice=5.E2*interaction1->nnu;
-// 	    thisnuexitice+=thisr_exitice;
-// 	    count1++;
-// 	  }
-// 	  if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>50.) {
-// 
-// 	    WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,50., // then back up and find it more precisely
-// 			     thisr_exitice);
-// 	    count1++;
-// 	  } // end third wheredoesitexit
-// 	  thisnuexitice=thisr_exitice;
-// 	} // if the exit point overshoots
-// 	else
-// 	  thisnuexitice=thisnuexitearth;
-// 
-// 	// should also correct for undershooting
+//  //cout << "inu is " << inu << " it's in ice.\n";
+//  //cout << "this is an ice bin.\n";
+//  thisnuexitice=thisnuexitearth;
+//  thisr_exitice=thisnuexitearth;
+//  if (thisnuexitice.Mag()>Surface(thisnuexitice)) { // if the exit point is above the surface
+//    if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>5.E3) {
+//      WhereDoesItExitIce(inu,thisnuexitearth,interaction1->nnu,5.E3, // then back up and find it more precisely
+//             thisr_exitice);
+//      thisnuexitice=(5000.)*interaction1->nnu;
+//      thisnuexitice+=thisr_exitice;
+//      count1++;
+//    }
+//    if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>5.E2) {
+//
+//      WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E2, // then back up and find it more precisely
+//             thisr_exitice);
+//      thisnuexitice=5.E2*interaction1->nnu;
+//      thisnuexitice+=thisr_exitice;
+//      count1++;
+//    }
+//    if ((thisnuexitice.Mag()-Surface(thisnuexitice))/cos(interaction1->nnu.Theta())>50.) {
+//
+//      WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,50., // then back up and find it more precisely
+//           thisr_exitice);
+//      count1++;
+//    } // end third wheredoesitexit
+//    thisnuexitice=thisr_exitice;
+//  } // if the exit point overshoots
+//  else
+//    thisnuexitice=thisnuexitearth;
+//
+//  // should also correct for undershooting
 //     if (count1>10)
-//       cout << "count1 is " << count1 << "\n";	  
+//       cout << "count1 is " << count1 << "\n";
 //       } // if it's an Antarctic ice bin
 //       else { // it leaves a rock bin so back up and find where it leaves ice
-// 	//cout << "inu is " << inu << " it's in rock.\n";
-// 	if (thisr_in.Distance(thisnuexitearth)>5.E4) {
-// 	  count2++;
-// 	  if (WhereDoesItExitIce(inu,thisnuexitearth,interaction1->nnu,5.E4, // then back up and find it more precisely
-// 				 thisr_exitice)) {
-// 	    
-// 	    thisnuexitice=(5.E4)*interaction1->nnu;
-// 	    thisnuexitice+=thisr_exitice;
-// 	    //cout << "inu is " << inu << " I'm here 1.\n";
-// 
-// 	  }
-// 	  else {
-// 	    interaction1->neverseesice=1;
+//  //cout << "inu is " << inu << " it's in rock.\n";
+//  if (thisr_in.Distance(thisnuexitearth)>5.E4) {
+//    count2++;
+//    if (WhereDoesItExitIce(inu,thisnuexitearth,interaction1->nnu,5.E4, // then back up and find it more precisely
+//         thisr_exitice)) {
+//
+//      thisnuexitice=(5.E4)*interaction1->nnu;
+//      thisnuexitice+=thisr_exitice;
+//      //cout << "inu is " << inu << " I'm here 1.\n";
+//
+//    }
+//    else {
+//      interaction1->neverseesice=1;
 //             interaction1->pickunbiased = 0;
-// 	    return 0;
-// 	  }
-// 	}
-// 	else
-// 	  thisnuexitice=thisnuexitearth;
-// 	//   WhereDoesItExitIce(inu,thisnuexit,interaction1->nnu,5.E4, // then back up and find it more precisely
-// // 			     thisr_exitice);
-// // 	  thisnuexit=5.E4*interaction1->nnu;
-// // 	  thisnuexit+=thisr_exitice;
-// 	if (thisr_in.Distance(thisnuexitice)>5.E3) {
-// 
-// 	  
-// 	  if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E3, // then back up and find it more precisely
-// 				  thisr_exitice)) {
-// 	    count2++;
-// 	    //interaction1->neverseesice=1;
-// 	    thisnuexitice=5.E3*interaction1->nnu;
-// 	    thisnuexitice+=thisr_exitice;
-// 	    //cout << "inu is " << inu << " I'm here 2\n";
-// 	    //return 0;
-// 	    
-// 	  }
-// 	}
-// 	if (thisr_in.Distance(thisnuexitice)>5.E2) {
-// 
-// 
-// 	  if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E2, // then back up and find it more precisely
-// 				  thisr_exitice)) {
-// 	    count2++;
-// 	    //interaction1->neverseesice=1;
-// 
-// 	    thisnuexitice=5.E2*interaction1->nnu;
-// 	    thisnuexitice+=thisr_exitice;
-// 	    //cout << "inu is " << inu << " I'm here 3\n";
-// 	    //return 0;
-// 	  }
-// 	
-// 	}
-// 	if (thisr_in.Distance(thisnuexitice)>50.) {
-// 
-// 
-// 	  if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,50., // then back up and find it more precisely
-// 				  thisr_exitice)) {
-// 	    //interaction1->neverseesice=1;
-// 	    count2++;
-// 	    //cout << "inu is " << inu << " I'm here 4\n";
-// 	    //return 0;
-// 	  }
-// 	}
-// 	thisnuexitice=thisr_exitice;
-// 	if (count2>10)
-// 	  cout << "count1 is " << count2 << "\n";
-// 	//	else return 0;  // never reaches any ice or is it because our step is too big
+//      return 0;
+//    }
+//  }
+//  else
+//    thisnuexitice=thisnuexitearth;
+//  //   WhereDoesItExitIce(inu,thisnuexit,interaction1->nnu,5.E4, // then back up and find it more precisely
+// //            thisr_exitice);
+// //     thisnuexit=5.E4*interaction1->nnu;
+// //     thisnuexit+=thisr_exitice;
+//  if (thisr_in.Distance(thisnuexitice)>5.E3) {
+//
+//
+//    if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E3, // then back up and find it more precisely
+//          thisr_exitice)) {
+//      count2++;
+//      //interaction1->neverseesice=1;
+//      thisnuexitice=5.E3*interaction1->nnu;
+//      thisnuexitice+=thisr_exitice;
+//      //cout << "inu is " << inu << " I'm here 2\n";
+//      //return 0;
+//
+//    }
+//  }
+//  if (thisr_in.Distance(thisnuexitice)>5.E2) {
+//
+//
+//    if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,5.E2, // then back up and find it more precisely
+//          thisr_exitice)) {
+//      count2++;
+//      //interaction1->neverseesice=1;
+//
+//      thisnuexitice=5.E2*interaction1->nnu;
+//      thisnuexitice+=thisr_exitice;
+//      //cout << "inu is " << inu << " I'm here 3\n";
+//      //return 0;
+//    }
+//
+//  }
+//  if (thisr_in.Distance(thisnuexitice)>50.) {
+//
+//
+//    if (WhereDoesItExitIce(inu,thisnuexitice,interaction1->nnu,50., // then back up and find it more precisely
+//          thisr_exitice)) {
+//      //interaction1->neverseesice=1;
+//      count2++;
+//      //cout << "inu is " << inu << " I'm here 4\n";
+//      //return 0;
+//    }
+//  }
+//  thisnuexitice=thisr_exitice;
+//  if (count2>10)
+//    cout << "count1 is " << count2 << "\n";
+//  //  else return 0;  // never reaches any ice or is it because our step is too big
 //       } // if the nu leaves a rock bin
 //     } // end wheredoesitleave
 //     else {
@@ -445,30 +523,30 @@ Position IceModel::PickBalloonPosition() const {
 //       return 0;
 //     }
 //     // end finding where it leaves ice
-// 
-// // 	if (thisnuexit.Mag()<Surface(thisnuexit)) { // if the exit point is below the surface
-// // 	  WhereDoesItExitIceForward(thisnuexit,interaction1->nnu,20., // then find it more finely
-// // 			     thisr_exitice);
-// // 	  thisnuexit=thisr_enterice;
-// // 	  // then back up and find it more precisely
-// // 	}
-// 
+//
+// //   if (thisnuexit.Mag()<Surface(thisnuexit)) { // if the exit point is below the surface
+// //     WhereDoesItExitIceForward(thisnuexit,interaction1->nnu,20., // then find it more finely
+// //            thisr_exitice);
+// //     thisnuexit=thisr_enterice;
+// //     // then back up and find it more precisely
+// //   }
+//
 //     if (WhereDoesItEnterIce(thisnuexitearth,interaction1->nnu,5.E3, // first pass with sort of course binning
-// 			    thisr_enterice)) {
+//          thisr_enterice)) {
 //       thisr_enterice_tmp=thisr_enterice+5.E3*interaction1->nnu;
 //       //cout << "inu is " << inu << " thisr_enterice is ";thisr_enterice.Print();
 //       if (WhereDoesItEnterIce(thisr_enterice_tmp,interaction1->nnu,20., // second pass with finer binning
-// 			      thisr_enterice)) {
-// 	//cout << "inu is " << inu << " thisr_enterice is ";thisr_enterice.Print();
-// 	//cout << "entersice is ";thisr_enterice.Print();
-// 	//cout << "thisnuexitice is ";thisnuexitice.Print();
-// 	interaction1->pathlength_inice=thisr_enterice.Distance(thisnuexitice);
-// 	//cout << "distance is " << distance << "\n";
-// 	//cout << "inu " << inu << " thisr_enterice, thisnuexitice are ";thisr_enterice.Print();thisnuexitice.Print();
-// 	interaction1->posnu=interaction1->pathlength_inice*gRandom->Rndm()*interaction1->nnu;
-// 	interaction1->posnu=interaction1->posnu+thisr_enterice;
-// 	//cout << "inu" << inu << " thisr_enterice, thisnuexitice are ";thisr_enterice.Print();thisnuexitice.Print();
-// 	//cout << "inu " << inu << " distance is " << distance << "\n";
+//            thisr_enterice)) {
+//  //cout << "inu is " << inu << " thisr_enterice is ";thisr_enterice.Print();
+//  //cout << "entersice is ";thisr_enterice.Print();
+//  //cout << "thisnuexitice is ";thisnuexitice.Print();
+//  interaction1->pathlength_inice=thisr_enterice.Distance(thisnuexitice);
+//  //cout << "distance is " << distance << "\n";
+//  //cout << "inu " << inu << " thisr_enterice, thisnuexitice are ";thisr_enterice.Print();thisnuexitice.Print();
+//  interaction1->posnu=interaction1->pathlength_inice*gRandom->Rndm()*interaction1->nnu;
+//  interaction1->posnu=interaction1->posnu+thisr_enterice;
+//  //cout << "inu" << inu << " thisr_enterice, thisnuexitice are ";thisr_enterice.Print();thisnuexitice.Print();
+//  //cout << "inu " << inu << " distance is " << distance << "\n";
 //       }
 //     }
 //     else {
@@ -479,7 +557,7 @@ Position IceModel::PickBalloonPosition() const {
 //     }
 //     interaction1->nuexitice=thisnuexitice;
 //     interaction1->r_enterice=thisr_enterice;
-//     
+//
 //     if (interaction1->posnu.Mag()-Surface(interaction1->posnu)>0) {
 //       interaction1->toohigh=1;
 //       //cout << "inu, toohigh is " << inu << " " << interaction1->toohigh << "\n";
@@ -491,25 +569,25 @@ Position IceModel::PickBalloonPosition() const {
 //       //cout << "inu, toolow is " << inu << " " << interaction1->toolow << "\n";
 //       interaction1->pickunbiased = 0;
 //       return 0;
-//     }    
+//     }
 //     interaction1->pickunbiased = 1;
 //     return 1;
-// 
+//
 // }
-//-------------------------------------------------- 
+//--------------------------------------------------
 
 
 //--------------------------------------------------
 // int IceModel::PickNear() {
 // }
-//-------------------------------------------------- 
+//--------------------------------------------------
 
 
 
 
 Vector IceModel::GetSurfaceNormal(const Position &r_out) const {
   Vector n_surf = r_out.Unit();
-  if (FLATSURFACE) 
+  if (FLATSURFACE)
     return n_surf;
 
   if (ice_model==0) {
@@ -517,29 +595,29 @@ Vector IceModel::GetSurfaceNormal(const Position &r_out) const {
 
     int ilon,ilat;
     GetILonILat(r_out,ilon,ilat);
-    
+
     int ilon_previous=ilon-1;
     if (ilon_previous<0)
       ilon_previous=NLON-1;
-    
+
     int ilon_next=ilon+1;
     if (ilon_next==NLON)
       ilon_next=0;
-    
+
     double r=(geoid[ilat]+surfacer[ilon][ilat])*sin(theta);
-    
+
     double slope_phi=(surfacer[ilon_next][ilat]-surfacer[ilon_previous][ilat])/(r*2*phistep);
-    
+
     int ilat_previous=ilat-1;
     if (ilat_previous<0)
       ilat_previous=0;
-    
+
     int ilat_next=ilat+1;
     if (ilat_next==NLAT)
       ilat_next=NLAT-1;
-     
+
     double slope_costheta=(surfacer[ilon][ilat_next]-surfacer[ilon][ilat_previous])/((geoid[ilat]+surfacer[ilon][ilat])*2*thetastep);
-    
+
     // first rotate n_surf according to tilt in costheta and position on continent - rotate around the y axis.
     double angle=atan(slope_costheta);
 
@@ -547,7 +625,7 @@ Vector IceModel::GetSurfaceNormal(const Position &r_out) const {
 
     // now rotate n_surf according to tilt in phi - rotate around the z axis.
     angle=atan(slope_phi);
-  
+
     n_surf = n_surf.RotateZ(angle);
   } //end if(Crust 2.0)
   else if (ice_model==1) {
@@ -562,8 +640,8 @@ Vector IceModel::GetSurfaceNormal(const Position &r_out) const {
     lat_next = lat + dist_to_check * (180 / (local_surface_elevation * PI)); //the latitude 7.5 km south of the interaction
     lat_prev = lat - dist_to_check * (180 / (local_surface_elevation * PI)); //the latitude 7.5 km north of the interaction
 
-    lon_next = lon + dist_to_check * (180 / (sin(lat*RADDEG) * local_surface_elevation * PI)); 
-    lon_prev = lon - dist_to_check * (180 / (sin(lat*RADDEG) * local_surface_elevation * PI)); 
+    lon_next = lon + dist_to_check * (180 / (sin(lat*RADDEG) * local_surface_elevation * PI));
+    lon_prev = lon - dist_to_check * (180 / (sin(lat*RADDEG) * local_surface_elevation * PI));
 
     if (lat_next > 90) {
       //cout<<"lat_next is > 90"<<endl;
@@ -589,29 +667,29 @@ Vector IceModel::GetSurfaceNormal(const Position &r_out) const {
       //cout << "lon_prev < 0";
       lon_prev += 360;
     }
-   
+
     double slope_phi=(SurfaceAboveGeoid(lon_next,lat)-SurfaceAboveGeoid(lon_prev,lat))/(2*dist_to_check);
 
     double slope_costheta=(SurfaceAboveGeoid(lon,lat_next)-SurfaceAboveGeoid(lon,lat_prev))/(2*dist_to_check);
-    
+
     // first rotate n_surf according to tilt in costheta - rotate around the y axis.
     double angle=atan(slope_costheta);
 
     n_surf = n_surf.RotateY(angle);
-   
+
     // now rotate n_surf according to tilt in phi - rotate around the z axis.
     angle=atan(slope_phi);
 
     n_surf = n_surf.RotateZ(angle);
   } //end if(BEDMAP)
-    
+
   return n_surf;
-    
+
 } //method GetSurfaceNormal
 
 Position IceModel::WhereDoesItEnterIce(const Position &posnu,
-				       const Vector &nnu,
-				       double stepsize) const {
+               const Vector &nnu,
+               double stepsize) const {
   // now get exit point...
   //   see my geometry notes.
   // parameterize the neutrino trajectory and just see where it
@@ -622,12 +700,12 @@ Position IceModel::WhereDoesItEnterIce(const Position &posnu,
   int left_edge=0;
   Position x = posnu;
   double x2;
-  
+
   Position x_previous = posnu;
 
   double x_previous2= x_previous * x_previous;
   x2=x_previous2;
-  
+
   double lon = x.Lon(),lat = x.Lat();
   double lon_old = lon,lat_old = lat;
   double local_surface = Surface(lon,lat);
@@ -651,22 +729,22 @@ Position IceModel::WhereDoesItEnterIce(const Position &posnu,
     if (lon!=lon_old || lat!=lat_old) {
       local_surface = Surface(lon,lat);
 
-      if (lat>COASTLINE) 
-	left_edge=1;
-      
+      if (lat>COASTLINE)
+  left_edge=1;
+
       rock2=pow((local_surface - IceThickness(lon,lat) - WaterDepth(lon,lat)),2);
-      surface2=pow(local_surface,2);    
+      surface2=pow(local_surface,2);
 
       if (ice_model==0) {
-	if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
-	  left_edge=1;
+  if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
+    left_edge=1;
       } //if (Crust 2.0)
     } //if (neutrino has stepped into new lon/lat bin)
 
     if ((x_previous2>rock_previous2 && x2<rock2)
-	|| (x_previous2<surface_previous2 && x2>surface2)
-	|| left_edge) {
-       
+  || (x_previous2<surface_previous2 && x2>surface2)
+  || left_edge) {
+
       r_enterice = x;
       // this gets you out of the loop.
       distance=3*Geoid(lat);
@@ -699,30 +777,30 @@ Position IceModel::WhereDoesItEnter(const Position &posnu,const Vector &nnu) con
     double p = posnu.Mag(); // radius of interaction
     double costheta = (nnu*posnu) / p; // theta of neutrino at interaction position
     double sintheta = sqrt(1-costheta*costheta);
-    
+
     double lon = posnu.Lon();
     double lat = posnu.Lat();
-    
+
     double a=0; // length of chord
-    
+
     double R = Surface(lon,lat);
     double delta = R - p; // depth of the interaction
     // if interaction occurs below surface, as it should
-    
+
     if (delta>-0.001) {
-	a=p*costheta+sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta); // chord length
-	if (a<0) {
-	    cout << "Negative chord length: " << a << "\n";
-	} //end if
-    } //end if (interaction below surface)  
+  a=p*costheta+sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta); // chord length
+  if (a<0) {
+      cout << "Negative chord length: " << a << "\n";
+  } //end if
+    } //end if (interaction below surface)
     else if (delta<=-0.001) {
-	
-	//cout << "Error in interaction position.  whichray is " << whichray << "\n";
-      //	cout << "lon, lat from WhereDoesItEnter is " << " " << lon << " " << lat << "\n";
-      //	cout << "geoid, surface, p, surface-p are " << Geoid(lat) << " " << Surface(lon,lat) << ", " << p << " , "<<(Surface(lon,lat)-p)<<"\n";
-	
+
+  //cout << "Error in interaction position.  whichray is " << whichray << "\n";
+      //  cout << "lon, lat from WhereDoesItEnter is " << " " << lon << " " << lat << "\n";
+      //  cout << "geoid, surface, p, surface-p are " << Geoid(lat) << " " << Surface(lon,lat) << ", " << p << " , "<<(Surface(lon,lat)-p)<<"\n";
+
     } //else if: error: interaction takes place above the surface
-    
+
     // first approx
     Position r_in = posnu - a*nnu;
 
@@ -732,7 +810,7 @@ Position IceModel::WhereDoesItEnter(const Position &posnu,const Vector &nnu) con
     //    delta = r_in.Mag() - Surface( r_in );
     //    r_in = r_in + (delta * nnu);
     //}
-    
+
     delta = r_in.Mag() - Surface( r_in );
     while ( fabs(delta) >= 0.1 ) {
         r_in = r_in + (delta * nnu);
@@ -745,12 +823,12 @@ Position IceModel::WhereDoesItEnter(const Position &posnu,const Vector &nnu) con
         }
     }
 
-    
+
     //lon = r_in.Lon();
     //lat = r_in.Lat();
-    
+
     //r_in = Surface(lon,lat) * r_in.Unit();
-    
+
     return r_in;
 } //method WhereDoesItEnter
 
@@ -764,40 +842,40 @@ int IceModel::WhereDoesItEnter_sphere(const Position &sphere_in, const Vector &n
     double p = sphere_in.Mag(); // radius of interaction
     double costheta = (nnu*sphere_in) / p; // theta of neutrino at interaction position
     double sintheta = sqrt(1-costheta*costheta);
-    
+
     double lon = sphere_in.Lon();
     double lat = sphere_in.Lat();
-    
+
     double a=0; // length of chord
-    
+
     double R = Surface(lon,lat);
     double delta = R - p; // depth of the interaction
     // if interaction occurs below surface, as it should
-    
+
 
 
     // if sphere_in is inside the earth
     if (delta>-0.001) {
-	//a=p*costheta+sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta); // chord length
-	a=p*costheta + sqrt(R*R-p*p*sintheta*sintheta); // chord length
-	if (a<0) {
-	    cout << "Negative chord length: " << a << "\n";
-	} //end if
+  //a=p*costheta+sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta); // chord length
+  a=p*costheta + sqrt(R*R-p*p*sintheta*sintheta); // chord length
+  if (a<0) {
+      cout << "Negative chord length: " << a << "\n";
+  } //end if
 
         // first approx
         r_in = sphere_in - a*nnu;
 
-    } //end if (sphere_in below surface)  
+    } //end if (sphere_in below surface)
 
     // if sphere_in is outside the earth
     else if (delta<=-0.001) {
-	
+
         // D : shortest distance between earth center and neutrino trajectory
         Position D = sphere_in + (p*costheta)*nnu;
 
         // neutrino pass through the earth
         if ( D.Mag() < Surface(D) ) {
-        
+
             // first approx
             r_in = sphere_in - (sqrt(R*R-D.Mag()*D.Mag())+costheta*p)*nnu;
         }
@@ -805,9 +883,9 @@ int IceModel::WhereDoesItEnter_sphere(const Position &sphere_in, const Vector &n
         else {
             return 0;
         }
-	
+
     } //else if (sphere_in above surface)
-    
+
 
     int iter = 0;
     // now do correction 3 times
@@ -815,7 +893,7 @@ int IceModel::WhereDoesItEnter_sphere(const Position &sphere_in, const Vector &n
     //    delta = r_in.Mag() - Surface( r_in );
     //    r_in = r_in + (delta * nnu);
     //}
-    
+
     delta = r_in.Mag() - Surface( r_in );
     while ( fabs(delta) >= 0.1 ) {
         r_in = r_in + (delta * nnu);
@@ -845,37 +923,37 @@ Position IceModel::WhereDoesItLeave(const Position &posnu,const Vector &nnu) con
     double p = posnu.Mag(); // radius of interaction
     double costheta = (nnu*posnu) / p; // theta of neutrino at interaction position
     double sintheta = sqrt(1-costheta*costheta);
-    
+
     double lon = posnu.Lon();
     double lat = posnu.Lat();
-    
+
     double a=0; // length of chord
-    
+
     double R = Surface(lon,lat);
     double delta = R - p; // depth of the interaction
     // if interaction occurs below surface, as it should
-    
+
     if (delta>-0.001) {
-	a=sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta) - p*costheta; // chord length
-	if (a<0) {
-	    cout << "Negative chord length: " << a << "\n";
-	} //end if
-    } //end if (interaction below surface)  
+  a=sqrt(R*R*costheta*costheta+2*delta*R*sintheta*sintheta) - p*costheta; // chord length
+  if (a<0) {
+      cout << "Negative chord length: " << a << "\n";
+  } //end if
+    } //end if (interaction below surface)
     else if (delta<=-0.001) {
-	
-	//cout << "Error in interaction position.  whichray is " << whichray << "\n";
-      //	cout << "lon, lat from WhereDoesItLeave is " << " " << lon << " " << lat << "\n";
-      //	cout << "geoid, surface, p, surface-p are " << Geoid(lat) << " " << Surface(lon,lat) << " " << p << " , "<<(Surface(lon,lat)-p)<<"\n";
-	
+
+  //cout << "Error in interaction position.  whichray is " << whichray << "\n";
+      //  cout << "lon, lat from WhereDoesItLeave is " << " " << lon << " " << lat << "\n";
+      //  cout << "geoid, surface, p, surface-p are " << Geoid(lat) << " " << Surface(lon,lat) << " " << p << " , "<<(Surface(lon,lat)-p)<<"\n";
+
     } //else if: error: interaction takes place above the surface
-    
+
     Position r_in = posnu + a*nnu;
-    
+
     lon = r_in.Lon();
     lat = r_in.Lat();
-    
+
     r_in = Surface(lon,lat) * r_in.Unit();
-    
+
     return r_in;
 } //method WhereDoesItLeave
 
@@ -886,66 +964,66 @@ Position IceModel::WhereDoesItLeave(const Position &posnu,const Vector &nnu) con
 // Below WhereDoesItEnterIce is from icemodel in icemc.
 //--------------------------------------------------
 // int IceModel::WhereDoesItEnterIce(const Position &posnu,
-// 				       const Vector &nnu,
-// 				       double stepsize,
-// 				       Position &r_enterice) {
+//               const Vector &nnu,
+//               double stepsize,
+//               Position &r_enterice) {
 //   // now get exit point...
 //   //   see my geometry notes.
 //   // parameterize the neutrino trajectory and just see where it
 //   // crosses the earth radius.
-// 
+//
 //   //  Position r_enterice;
 //   double distance=0;
 //   int left_edge=0;
 //   Position x = posnu;
 //   double x2;
-//   
+//
 //   Position x_previous = posnu;
-// 
+//
 //   double x_previous2= x_previous * x_previous;
 //   x2=x_previous2;
-//   
+//
 //   double lon = x.Lon(),lat = x.Lat();
 //   double lon_old = lon,lat_old = lat;
 //   double local_surface = Surface(lon,lat);
 //   double rock_previous2= pow((local_surface - IceThickness(lon,lat) - WaterDepth(lon,lat)),2);
 //   double surface_previous2=pow(local_surface,2);
-// 
+//
 //   double rock2=rock_previous2;
 //   double surface2=surface_previous2;
 //   int foundit=0;  // keeps track of whether you found an ice entrance point
-// 
+//
 //   //  cout << "lon, lat are " << posnu.Lon() << " " << posnu.Lat() << "\n";
 //   //cout << "x2 at start is " << x2 << "\n";
 //   while (distance<2*local_surface+1000) {
-// 
+//
 //     distance+=stepsize;
-// 
+//
 //     x -= stepsize*nnu;
 //     x2=x*x;
 //     //cout << "x2 is " << x2 << "\n";
 //     lon = x.Lon();
 //     lat = x.Lat();
-// 
+//
 //       double ice_thickness=IceThickness(lon,lat);
 //     if (lon!=lon_old || lat!=lat_old) {
 //       local_surface = Surface(lon,lat);
-// 
-//       //if (lat>COASTLINE) 
+//
+//       //if (lat>COASTLINE)
 //       //left_edge=1;
-// 
+//
 //       rock2=pow((local_surface - IceThickness(lon,lat) - WaterDepth(lon,lat)),2);
-//       surface2=pow(local_surface,2);    
-// 
+//       surface2=pow(local_surface,2);
+//
 //       if (ice_model==0) {
-// 	if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
-// 	  left_edge=1;
+//  if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
+//    left_edge=1;
 //       } //if (Crust 2.0)
 //     } //if (neutrino has stepped into new lon/lat bin)
-// 
+//
 //     if ((((x_previous2>rock_previous2 && x2<rock2) // crosses rock boundary from above
-// 	 || (x_previous2<surface_previous2 && x2>surface2)) && ice_thickness>0 && lat<COASTLINE) // crosses surface boundary from below
-// 	|| left_edge) {
+//   || (x_previous2<surface_previous2 && x2>surface2)) && ice_thickness>0 && lat<COASTLINE) // crosses surface boundary from below
+//  || left_edge) {
 //       //  cout << "lat, COASTLINE, left_edge is " << lat << " " << COASTLINE<< " " << left_edge << "\n";
 //       //cout << "x_previous2, surface_previous, x2, surface2 are " << x_previous2 << " " << surface_previous2 << " " << x2 << " " << surface2 << "\n";
 //       r_enterice = x;
@@ -957,65 +1035,65 @@ Position IceModel::WhereDoesItLeave(const Position &posnu,const Vector &nnu) con
 //       //cout << "r_enterice is ";r_enterice.Print();
 //       //continue;
 //     } //if
-// 
+//
 //     x_previous = x;
 //     x_previous2 = x2;
 //     //cout << "x_previous, x_previous2 " << x << " " << x2 << "\n";
-// 
+//
 //     if (lon!=lon_old || lat!=lat_old) {
 //       rock_previous2 = rock2;
 //       surface_previous2 = surface2;
 //       lat_old = lat;
 //       lon_old = lon;
 //     } //if
-// 
+//
 //   } //while
-// 
+//
 //   return foundit;
 // }//WhereDoesItEnterIce
-// 
-// 
-// 
-// 
+//
+//
+//
+//
 // int IceModel::WhereDoesItExitIce(int inu,const Position &posnu,
-// 				       const Vector &nnu,
-// 				       double stepsize,
-// 				       Position &r_enterice) {
+//               const Vector &nnu,
+//               double stepsize,
+//               Position &r_enterice) {
 //   // now get exit point...
 //   //   see my geometry notes.
 //   // parameterize the neutrino trajectory and just see where it
 //   // crosses the earth radius.
-// 
+//
 //   //  Position r_enterice;
 //   double distance=0;
 //   int left_edge=0;
 //   Position x = posnu;
 //   double x2;
-//   
+//
 //   if (inu==1491) {
-//    
+//
 //     cout << "posnu is";posnu.Print();
 //     cout << "nnu is ";nnu.Print();
 //   }
-//    
-// 
+//
+//
 //   Position x_previous = posnu;
-// 
+//
 //   double x_previous2= x_previous * x_previous;
 //   x2=x_previous2;
-//   
+//
 //   double lon = x.Lon(),lat = x.Lat();
 //   double lon_old = lon,lat_old = lat;
 //   double local_surface = Surface(lon,lat);
 //   double rock_previous2= pow((local_surface - IceThickness(lon,lat) - WaterDepth(lon,lat)),2);
 //   double surface_previous2=pow(local_surface,2);
-// 
+//
 //   double rock2=rock_previous2;
 //   double surface2=surface_previous2;
 //   int foundit=0;  // keeps track of whether you found an ice entrance point
-// 
-//  
-// 
+//
+//
+//
 //   //  cout << "lon, lat are " << posnu.Lon() << " " << posnu.Lat() << "\n";
 //   //cout << "x2 at start is " << x2 << "\n";
 //   int nsteps=0;
@@ -1029,29 +1107,29 @@ Position IceModel::WhereDoesItLeave(const Position &posnu,const Vector &nnu) con
 //     //cout << "x2 is " << x2 << "\n";
 //     lon = x.Lon();
 //     lat = x.Lat();
-// 
+//
 //       double ice_thickness=IceThickness(lon,lat);
 //     if (lon!=lon_old || lat!=lat_old) {
 //       local_surface = Surface(lon,lat);
-// 
-//       //if (lat>COASTLINE) 
+//
+//       //if (lat>COASTLINE)
 //       //left_edge=1;
-// 
+//
 //       rock2=pow((local_surface - IceThickness(lon,lat) - WaterDepth(lon,lat)),2);
-//       surface2=pow(local_surface,2);    
-// 
+//       surface2=pow(local_surface,2);
+//
 //       if (ice_model==0) {
-// 	if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
-// 	  left_edge=1;
+//  if ((int)(lat)==COASTLINE && rock_previous2 < x2 && surface2 > x2)
+//    left_edge=1;
 //       } //if (Crust 2.0)
 //     } //if (neutrino has stepped into new lon/lat bin)
-// 
+//
 //     if (inu==1491 && nsteps<10)
 //       cout << "inu, x_previous2, rock_previous2, x2, rock2 are " << inu << " " << x_previous2 << " " << rock_previous2 << " " << x2 << " " << rock2 << "\n";
-// 
+//
 //     if ((((x_previous2<rock_previous2 && x2>rock2) // crosses rock boundary from above
-// 	 || (x_previous2>surface_previous2 && x2<surface2)) && ice_thickness>0 && lat<COASTLINE) // crosses surface boundary from above
-// 	|| left_edge) {
+//   || (x_previous2>surface_previous2 && x2<surface2)) && ice_thickness>0 && lat<COASTLINE) // crosses surface boundary from above
+//  || left_edge) {
 //       //  cout << "lat, COASTLINE, left_edge is " << lat << " " << COASTLINE<< " " << left_edge << "\n";
 //       //cout << "x_previous2, surface_previous, x2, surface2 are " << x_previous2 << " " << surface_previous2 << " " << x2 << " " << surface2 << "\n";
 //       r_enterice = x;
@@ -1062,24 +1140,24 @@ Position IceModel::WhereDoesItLeave(const Position &posnu,const Vector &nnu) con
 //       //cout << "foundit is " << foundit << "\n";
 //       //continue;
 //     } //if
-// 
+//
 //     x_previous = x;
 //     x_previous2 = x2;
 //     //cout << "x_previous, x_previous2 " << x << " " << x2 << "\n";
-// 
+//
 //     if (lon!=lon_old || lat!=lat_old) {
 //       rock_previous2 = rock2;
 //       surface_previous2 = surface2;
 //       lat_old = lat;
 //       lon_old = lon;
 //     } //if
-// 
+//
 //   } //while
 //   if (inu==0) {
 //     cout << "r_enterice is ";r_enterice.Print();}
 //   return foundit;
 // }//WhereDoesItExitIce
-//-------------------------------------------------- 
+//--------------------------------------------------
 
 
 
@@ -1201,7 +1279,7 @@ int IceModel::RossExcept(const Position &pos) const{
   GetILonILat(pos,ilon,ilat);
 if(ilon<=178&&ilon>=174&&ilat>=4&&ilat<=5)
     return 1;
-  else 
+  else
     return 0;
 }
 
@@ -1262,9 +1340,9 @@ double IceModel::GetN(double altitude) const {
   double b1=0.0140157;
   double n=0;
 
-  if (altitude < FIRNDEPTH) 
+  if (altitude < FIRNDEPTH)
     n=NICE;
-  else if (altitude >= FIRNDEPTH && altitude <=0 && DEPTH_DEPENDENT_N) 
+  else if (altitude >= FIRNDEPTH && altitude <=0 && DEPTH_DEPENDENT_N)
     //    N_DEPTH=NFIRN-(4.6198+13.62*(altitude_int/1000.))*
     //(altitude_int/1000.);   // Besson's equation for n(z)
     n=NFIRN+a1*(1.0-exp(b1*altitude));   // Peter's equation for n(z)
@@ -1283,61 +1361,61 @@ double IceModel::GetN(const Position &pos) const{
 double IceModel::EffectiveAttenuationLength(const Position &pos,const int &whichray) const {
   double localmaxdepth = IceThickness(pos);
   double depth = Surface(pos) - pos.Mag();
-  
+
   int depth_index=0;
   double attenuation_length=0.0;
 //   if (inu<10) {
 //     cout << "pos is ";pos.Print();
 //     cout << "surface is " << Surface(pos) << "\n";
 //   }
-  if(WestLand(pos) && !CONSTANTICETHICKNESS) 
+  if(WestLand(pos) && !CONSTANTICETHICKNESS)
     {
       depth_index=int(depth*419.9/localmaxdepth);//use 420 m ice shelf attenuation length data as the standard, squeeze or stretch if localmaxdepth is longer or shorter than 420m.
-      if(RossIceShelf(pos) || RonneIceShelf(pos)) 
-	{	  
-	  if(whichray==0)
-	    attenuation_length=l_shelfup[depth_index];
-	  else if(whichray==1)
-	    attenuation_length=l_shelfdown[depth_index];
-	  else
-	    cerr << " wrong attenuation length " <<endl;
-	  
-	  //for sanity check
-	  if((depth_index+0.5)!=d_shelfup[depth_index])
-	    {
-	      cerr << "the index of the array l_iceshelfup is wrong!" << endl;
-	      exit(1);
-	    }
-	}
+      if(RossIceShelf(pos) || RonneIceShelf(pos))
+  {
+    if(whichray==0)
+      attenuation_length=l_shelfup[depth_index];
+    else if(whichray==1)
+      attenuation_length=l_shelfdown[depth_index];
+    else
+      cerr << " wrong attenuation length " <<endl;
+
+    //for sanity check
+    if((depth_index+0.5)!=d_shelfup[depth_index])
+      {
+        cerr << "the index of the array l_iceshelfup is wrong!" << endl;
+        exit(1);
+      }
+  }
       else //in ice sheet of westland
-	{
-	  if(whichray==0)
-	    attenuation_length=l_westlandup[depth_index]; 
-	  else if(whichray==1)
-	    attenuation_length=l_westlanddown[depth_index];
-	  else
-	    cerr << " wrong attenuation length " <<endl;
-      	}
-       
+  {
+    if(whichray==0)
+      attenuation_length=l_westlandup[depth_index];
+    else if(whichray==1)
+      attenuation_length=l_westlanddown[depth_index];
+    else
+      cerr << " wrong attenuation length " <<endl;
+        }
+
       if(mooreBayFlag)//if use Moore's Bay measured data for the west land
-	attenuation_length*=1.717557; //about 450 m (field attenuation length) for one whole way when assuming -3dB for the power loss at the bottom
+  attenuation_length*=1.717557; //about 450 m (field attenuation length) for one whole way when assuming -3dB for the power loss at the bottom
     }
   else //in east antarctica or constant ice thickness
-     { 
+     {
 //        if (inu<10) {
 //        cout << "localmaxdepth is " << localmaxdepth << "\n";
 //        cout << "depth is " << depth << "\n";
 //        }
        depth_index =int(depth*(2809.9/localmaxdepth));
        //if (inu<10)
-	 //       cout << "depth_index is " << depth_index << "\n";
+   //       cout << "depth_index is " << depth_index << "\n";
 
        if(whichray==0)
-	 attenuation_length =l_sheetup[depth_index];
+   attenuation_length =l_sheetup[depth_index];
        else if(whichray==1)
-	 attenuation_length =l_sheetdown[depth_index];
+   attenuation_length =l_sheetdown[depth_index];
        else
-	 cerr << " wrong attenuation length " <<endl;
+   cerr << " wrong attenuation length " <<endl;
      } //else
 
   return attenuation_length;
@@ -1347,62 +1425,62 @@ double IceModel::EffectiveAttenuationLength(const Position &pos,const int &which
 double IceModel::EffectiveAttenuationLength(Settings *settings1, const Position &pos,const int &whichray) const {
   double localmaxdepth = IceThickness(pos);
   double depth = Surface(pos) - pos.Mag();
-  
+
   int depth_index=0;
   double attenuation_length=0.0;
 //   if (inu<10) {
 //     cout << "pos is ";pos.Print();
 //     cout << "surface is " << Surface(pos) << "\n";
 //   }
-  if(WestLand(pos) && !CONSTANTICETHICKNESS) 
+  if(WestLand(pos) && !CONSTANTICETHICKNESS)
     {
       depth_index=int(depth*419.9/localmaxdepth);//use 420 m ice shelf attenuation length data as the standard, squeeze or stretch if localmaxdepth is longer or shorter than 420m.
-      if(RossIceShelf(pos) || RonneIceShelf(pos)) 
-	{	  
-	  if(whichray==0)
-	    attenuation_length=l_shelfup[depth_index];
-	  else if(whichray==1)
-	    attenuation_length=l_shelfdown[depth_index];
-	  else
-	    cerr << " wrong attenuation length " <<endl;
-	  
-	  //for sanity check
-	  if((depth_index+0.5)!=d_shelfup[depth_index])
-	    {
-	      cerr << "the index of the array l_iceshelfup is wrong!" << endl;
-	      exit(1);
-	    }
-	}
+      if(RossIceShelf(pos) || RonneIceShelf(pos))
+  {
+    if(whichray==0)
+      attenuation_length=l_shelfup[depth_index];
+    else if(whichray==1)
+      attenuation_length=l_shelfdown[depth_index];
+    else
+      cerr << " wrong attenuation length " <<endl;
+
+    //for sanity check
+    if((depth_index+0.5)!=d_shelfup[depth_index])
+      {
+        cerr << "the index of the array l_iceshelfup is wrong!" << endl;
+        exit(1);
+      }
+  }
       else //in ice sheet of westland
-	{
-	  if(whichray==0)
-	    attenuation_length=l_westlandup[depth_index]; 
-	  else if(whichray==1)
-	    attenuation_length=l_westlanddown[depth_index];
-	  else
-	    cerr << " wrong attenuation length " <<endl;
-      	}
-       
+  {
+    if(whichray==0)
+      attenuation_length=l_westlandup[depth_index];
+    else if(whichray==1)
+      attenuation_length=l_westlanddown[depth_index];
+    else
+      cerr << " wrong attenuation length " <<endl;
+        }
+
       //if(mooreBayFlag)//if use Moore's Bay measured data for the west land
       if(settings1->MOOREBAY)//if use Moore's Bay measured data for the west land
-	attenuation_length*=1.717557; //about 450 m (field attenuation length) for one whole way when assuming -3dB for the power loss at the bottom
+  attenuation_length*=1.717557; //about 450 m (field attenuation length) for one whole way when assuming -3dB for the power loss at the bottom
     }
   else //in east antarctica or constant ice thickness
-     { 
+     {
 //        if (inu<10) {
 //        cout << "localmaxdepth is " << localmaxdepth << "\n";
 //        cout << "depth is " << depth << "\n";
 //        }
        depth_index =int(depth*(2809.9/localmaxdepth));
        //if (inu<10)
-	 //       cout << "depth_index is " << depth_index << "\n";
+   //       cout << "depth_index is " << depth_index << "\n";
 
        if(whichray==0)
-	 attenuation_length =l_sheetup[depth_index];
+   attenuation_length =l_sheetup[depth_index];
        else if(whichray==1)
-	 attenuation_length =l_sheetdown[depth_index];
+   attenuation_length =l_sheetdown[depth_index];
        else
-	 cerr << " wrong attenuation length " <<endl;
+   cerr << " wrong attenuation length " <<endl;
      } //else
 
   return attenuation_length;
@@ -1413,7 +1491,7 @@ double IceModel::EffectiveAttenuationLength(Settings *settings1, const Position
 
 
 double IceModel::Area(double latitude) const {
-  //Returns the area of one square of the BEDMAP data at a given latitude. 
+  //Returns the area of one square of the BEDMAP data at a given latitude.
   double lat_rad = (90 - latitude) * RADDEG;
 
   return (pow(cellSize* ((1 + sin(71*RADDEG)) / (1 + sin(lat_rad))),2));
@@ -1501,7 +1579,7 @@ void IceModel::ENtoLonLat(int e_coord, int n_coord, double xLowerLeft, double yL
   //  if (lon>160 && lon<165)
   //cout << "e_coord, n_coord, easting, northing, lon are " << e_coord << " " << n_coord << " " << easting << " " << northing << " " << lon << "\n";
   return;
-  
+
 } //method ENtoLonLat
 
 void IceModel::IceENtoLonLat(int e, int n, double& lon, double& lat) const {
@@ -1538,11 +1616,11 @@ void IceModel::ReadIceThickness() {
   string tempBuf5;
   string tempBuf6;
   int temp1,temp2,temp3,temp4,temp5,temp6;
-  
-  IceThicknessFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2 
-		   >> tempBuf3 >> temp3 >> tempBuf4 >> temp4 
-		   >> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
-  
+
+  IceThicknessFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2
+       >> tempBuf3 >> temp3 >> tempBuf4 >> temp4
+       >> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
+
   if(tempBuf1 == string("ncols")) {
     nCols_ice=temp1;
   }
@@ -1563,17 +1641,17 @@ void IceModel::ReadIceThickness() {
   }
   //cout<<"nCols_ice, nRows_ice "<<nCols_ice<<" , "<<nRows_ice<<endl;
   //cout<<"xLL_ice, yLL_ice, cellsize "<<xLowerLeft_ice<<" , "<<yLowerLeft_ice<<" , "<<cellSize<<endl<<endl;
-  
+
   double theValue;
   for(int rowNum=0;rowNum<nRows_ice;rowNum++) {
     for(int colNum=0;colNum<nCols_ice;colNum++) {
       IceThicknessFile >> theValue;
       if(theValue==NODATA)
-	theValue=0; //Set ice depth to 0 where we have no data.
+  theValue=0; //Set ice depth to 0 where we have no data.
       ice_thickness_array[colNum][rowNum] = double(theValue); //This stores data as ice_thickness_array[easting][northing]
     }//for
   }//for
-  
+
   IceThicknessFile.close();
   return;
 } //method ReadIceThickness
@@ -1595,11 +1673,11 @@ void IceModel::ReadGroundBed() {
   string tempBuf5;
   string tempBuf6;
   int temp1,temp2,temp3,temp4,temp5,temp6;
-  
-  GroundBedFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2 
-		>> tempBuf3 >> temp3 >> tempBuf4 >> temp4 
-		>> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
-  
+
+  GroundBedFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2
+    >> tempBuf3 >> temp3 >> tempBuf4 >> temp4
+    >> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
+
   if(tempBuf1 == string("ncols")) {
     nCols_ground=temp1;
   }
@@ -1621,20 +1699,20 @@ void IceModel::ReadGroundBed() {
 
   //cout<<"nCols_ground, nRows_ground "<<nCols_ground<<" , "<<nRows_ground<<endl;
   //cout<<"xLL_ground, yLL_ground, cellsize "<<xLowerLeft_ground<<" , "<<yLowerLeft_ground<<" , "<<cellSize<<endl<<endl;
-  
+
   double theValue;
   for(int rowNum=0;rowNum<nRows_ground;rowNum++) {
     for(int colNum=0;colNum<nCols_ground;colNum++) {
       GroundBedFile >> theValue;
-      
+
       if(theValue==NODATA)
-	theValue=0; //Set elevation to 0 where we have no data.
+  theValue=0; //Set elevation to 0 where we have no data.
       ground_elevation[colNum][rowNum] = double(theValue);
       //if (theValue != -96 && theValue != 0)
       //cout<<"ground_elevation: "<<theValue<<endl;
     }//for
   }//for
-  
+
   GroundBedFile.close();
   return;
 } //method ReadGroundBed
@@ -1656,11 +1734,11 @@ void IceModel::ReadWaterDepth() {
   string tempBuf5;
   string tempBuf6;
   int temp1,temp2,temp3,temp4,temp5,temp6;
-  
-  WaterDepthFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2 
-		 >> tempBuf3 >> temp3 >> tempBuf4 >> temp4 
-		 >> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
-  
+
+  WaterDepthFile >> tempBuf1 >> temp1 >> tempBuf2 >> temp2
+     >> tempBuf3 >> temp3 >> tempBuf4 >> temp4
+     >> tempBuf5 >> temp5 >> tempBuf6 >> temp6;
+
   if(tempBuf1 == string("ncols")) {
     nCols_water=temp1;
   }
@@ -1682,18 +1760,18 @@ void IceModel::ReadWaterDepth() {
 
   //cout<<"nCols_water, nRows_water "<<nCols_water<<" , "<<nRows_water<<endl;
   //cout<<"xLL_water, yLL_water, cellsize "<<xLowerLeft_water<<" , "<<yLowerLeft_water<<" , "<<cellSize<<endl<<endl;
-  
+
   double theValue;
   for(int rowNum=0;rowNum<nRows_water;rowNum++) {
     for(int colNum=0;colNum<nCols_water;colNum++) {
       WaterDepthFile >> theValue;
-      
+
       if(theValue==NODATA)
-	theValue=0; //Set depth to 0 where we have no data.
+  theValue=0; //Set depth to 0 where we have no data.
       water_depth[colNum][rowNum] = double(theValue);
     }//for
   }//for
-  
+
   WaterDepthFile.close();
   return;
 } //method ReadWaterDepth
@@ -1809,7 +1887,7 @@ void IceModel::GetFresnel (
 
 //void IceModel::FillArraysforTree(double icethck[1200][1000],double elev[1068][869],double lon_ground[1068][869],double lat_ground[1068][869],double lon_ice[1200][1000],double lat_ice[1200][1000],double h20_depth[1200][1000],double lon_water[1200][1000],double lat_water[1200][1000]) {
 // void IceModel::FillArraysforTree(double lon_ground[1068][869],double lat_ground[1068][869],double lon_ice[1200][1000],double lat_ice[1200][1000],double lon_water[1200][1000],double lat_water[1200][1000]) {
- 
+
   //  for (int rowNum=0;rowNum<nRows_ice;rowNum++) {
   //for (int colNum=0;colNum<nCols_ice;colNum++) {
 //   for (int i=0;i<nRows_ice;i++) {
@@ -1820,7 +1898,7 @@ void IceModel::GetFresnel (
 //       //      cout << "lon_ice is " << rowNum << " " << colNum << " " << lon_ice[rowNum][colNum] << "\n";
 //       //this->IceENtoLonLat(i,j,test1,test2); //Recall that the e / n coordinates in horizon were picked from the ground bed array.
 //       //icethck[colNum][rowNum]=IceThickness(lon_ice[colNum][rowNum],lat_ice[colNum][rowNum]);
-     
+
 //       //      WaterENtoLonLat(colNum,rowNum,lon_water[colNum][rowNum],lat_water[colNum][rowNum]);
 //       //h20_depth[colNum][rowNum]=WaterDepth(lon_water[colNum][rowNum],lat_water[colNum][rowNum]);
 
diff --git a/IceModel.h b/IceModel.h
index 01e0da2e..e4adb14b 100644
--- a/IceModel.h
+++ b/IceModel.h
@@ -27,49 +27,49 @@ class IceModel : public EarthModel {
   int mooreBayFlag;
 
   //Information on horizons - what ice the balloon can see at each position along its path.
- 
- 
+
+
 //   double volume_inhorizon_average; // average volume of ice seen by balloon
 //   vector<int> ilon_inhorizon[NBNPOSITIONS_MAX]; // indices in lon and lat for bins in horizon for NPHI balloon positions along 80 deg latitude line.
 //   vector<int> ilat_inhorizon[NBNPOSITIONS_MAX];
 //   vector<int> easting_inhorizon[NBNPOSITIONS_MAX]; //indicies in easting and northing for bins in horizon for NPHI balloon positions along 80 deg latitude line.
 //   vector<int> northing_inhorizon[NBNPOSITIONS_MAX];
-//   double maxvol_inhorizon[NBNPOSITIONS_MAX]; // maximum volume of ice for a bin 
+//   double maxvol_inhorizon[NBNPOSITIONS_MAX]; // maximum volume of ice for a bin
 
   //BEDMAP utility methods
   double Area(double latitude) const;
 
-void ENtoLonLat(int e_coord, 
+void ENtoLonLat(int e_coord,
 		  int n_coord,
 		  double xLowerLeft,
 		  double yLowerLeft,
-		  
-		  double& lon, 
+
+		  double& lon,
 		  double& lat) const;
 
 
 
   void WaterENtoLonLat(int e,
 		       int n,
-		       
+
 		       double& lon,
 		       double& lat) const;
-  void LonLattoEN(double lon, 
+  void LonLattoEN(double lon,
 		  double lat,
 		  double xLowerLeft,
 		  double yLowerLeft,
-		
-		  int& e_coord, 
+
+		  int& e_coord,
 		  int& n_coord) const;
- 
-  void GroundLonLattoEN(double lon, 
+
+  void GroundLonLattoEN(double lon,
 			double lat,
-			
-			int& e_coord, 
+
+			int& e_coord,
 			int& n_coord) const;
   void WaterLonLattoEN(double lon,
 		       double lat,
-		       
+
 		       int& e_coord,
 		       int& n_coord) const;
 
@@ -107,22 +107,22 @@ void ENtoLonLat(int e_coord,
 
   void IceENtoLonLat(int e,
 		     int n,
-		     
+
 		     double& lon,
-		     double& lat) const;  
+		     double& lat) const;
   void GroundENtoLonLat(int e,
 			int n,
-			
+
 			double& lon,
 			double& lat) const;
 
   //  const static int NBNPOSITIONS_MAX=26000;
-  //double volume_inhorizon[NBNPOSITIONS_MAX]; // volume of ice within horizon for each balloon phi position 
+  //double volume_inhorizon[NBNPOSITIONS_MAX]; // volume of ice within horizon for each balloon phi position
 //  IceModel();   //default constructor
-  IceModel(int model=0,int earth_model=0,int mooreBay=0);
+  IceModel(int model=0,int earth_model=0,int mooreBay=0, int SYSTEMATICS_IceAtten = 0);
   ~IceModel();
 
-  void setUpIceModel(int model=0);
+  void setUpIceModel(int model=0, int SYSTEMATICS_IceAtten=0);
   double IceThickness(double lon,double lat) const;
   double IceThickness(const Position& pos) const;
   double Surface(double lon,double lat) const;
@@ -134,12 +134,12 @@ void ENtoLonLat(int e_coord,
 
   Position PickBalloonPosition() const;
   //void GetMAXHORIZON(double bn_altitude); // get upper limit on the horizon wrt the balloon.
-  int RossIceShelf(const Position &position) const; 
+  int RossIceShelf(const Position &position) const;
   int IceOnWater(const Position &postition) const;
   int RossExcept(const Position &position) const;
   int RonneIceShelf(const Position &position) const;
-  int WestLand(const Position &pos) const; 
-  int AcceptableRfexit(const Vector &nsurf_rfexit,const Position &rfexit,const Vector &n_exit2rx) const; 
+  int WestLand(const Position &pos) const;
+  int AcceptableRfexit(const Vector &nsurf_rfexit,const Position &rfexit,const Vector &n_exit2rx) const;
   //double GetBalloonPositionWeight(int ibnpos) const;
   int OutsideAntarctica(const Position &pos) const;
   int OutsideAntarctica(double lat) const;
@@ -160,11 +160,11 @@ void ENtoLonLat(int e_coord,
   double GetN(const Position &pos) const;
   double EffectiveAttenuationLength(const Position &pos, const int &whichray) const;
   double EffectiveAttenuationLength(Settings *settings1, const Position &pos, const int &whichray) const;
-  
-  void IceLonLattoEN(double lon, 
+
+  void IceLonLattoEN(double lon,
 		     double lat,
-		     
-		     int& e_coord, 
+
+		     int& e_coord,
 		     int& n_coord) const;
   int Getice_model();
 
@@ -183,7 +183,6 @@ void GetFresnel (
   int ARA_IceAtten_bin;
 
   double GetARAIceAttenuLength(double depth);
-
   //  void FillArraysforTree(double lon_ground[1068][869],double lat_ground[1068][869],double lon_ice[1200][1000],double lat_ice[1200][1000],double lon_water[1200][1000],double lat_water[1200][1000]);
 
   // below three members are copied from icemc icemodel.
@@ -194,12 +193,12 @@ void GetFresnel (
 // 			       const Vector &nnu,
 // 			       double stepsize,
 // 			       Position &r_enterice);
-// 
+//
 //   int WhereDoesItExitIce(int inu,const Position &posnu,
 // 			 const Vector &nnu,
 // 			 double stepsize,
 // 			 Position &r_enterice);
-//-------------------------------------------------- 
+//--------------------------------------------------
   // end three copied members from icemc icemodel.
 
 
diff --git a/Primaries.cc b/Primaries.cc
index 9220bb46..f95cb45c 100644
--- a/Primaries.cc
+++ b/Primaries.cc
@@ -258,16 +258,216 @@ Primaries::Primaries(){//constructor
   ymax_low=1.E-3;
   ymin_high=ymax_low;
   ymax_high=1.;
+
+  // cooper-sarkar cross-section version
+
+  vector<double> energy; // energy [GeV]
+  vector<double> nu_cc;    // nu cc cross section [pb]
+  vector<double> nu_cc_ul; // nu cc cross section upper limit [pb]
+  vector<double> nu_cc_ll; // nu cc cross section lower limit [pb]
+  vector<double> nu_cc_uu; // nu cc cross section upper uncertainties [%]
+  vector<double> nu_cc_lu; // nu cc cross section lower uncertainties [%]
+  vector<double> nu_nc;    // nu nc cross section
+  vector<double> nu_nc_ul; // nu nc cross section upper limit [pb]
+  vector<double> nu_nc_ll; // nu nc cross section lower limit [pb]
+  vector<double> nu_nc_uu; // nu cc cross section upper uncertainties [%]
+  vector<double> nu_nc_lu; // nu cc cross section lower uncertainties [%]
+
+  vector<double> nubar_cc;    // nubar cc cross section [pb]
+  vector<double> nubar_cc_ul; // nubar cc cross section upper limit [pb]
+  vector<double> nubar_cc_ll; // nubar cc cross section lower limit [pb]
+  vector<double> nubar_cc_uu; // nu cc cross section upper uncertainties [%]
+  vector<double> nubar_cc_lu; // nu cc cross section lower uncertainties [%]
+  vector<double> nubar_nc;    // nubar nc cross section [pb]
+  vector<double> nubar_nc_ul; // nubar nc cross section upper limit [pb]
+  vector<double> nubar_nc_ll; // nubar nc cross section lower limit [pb]
+  vector<double> nubar_nc_uu; // nu cc cross section upper uncertainties [%]
+  vector<double> nubar_nc_lu; // nu cc cross section lower uncertainties [%]
+
+  // first, load the neutrino (nu) cross sections
+  ifstream fin_nu("./data/coopersarkar_sigma_nu.csv");
+  string line;
+  if(fin_nu.is_open()){
+    while(fin_nu.good()){
+      getline(fin_nu, line);
+      stringstream s_stream(line);
+      vector<double> result;
+      while(s_stream.good()){
+        string substr;
+        getline(s_stream, substr, ',');
+        result.push_back(atof(substr.c_str()));
+      }
+      energy.push_back(result[0]); // energy
+      
+      nu_cc.push_back(result[1]); // charged current cross-section
+      double cc_ul = (result[2]); 
+      double cc_ll = (result[4]); 
+      nu_cc_uu.push_back(cc_ul);
+      nu_cc_lu.push_back(cc_ll);
+      cc_ul/=100.; // convert from % to fraction
+      cc_ll/=100.; // convert from % to fraction
+      cc_ul+=1.; // 1 + upper uncertainty on cc (result[2]>0)
+      cc_ll+=1.; // 1 + lower uncertainty on cc (result[4]<0)
+      nu_cc_ul.push_back(result[1]*cc_ul);
+      nu_cc_ll.push_back(result[1]*cc_ll);
+
+      
+      nu_nc.push_back(result[5]); // neutral current cross-section
+      double nc_ul = (result[6]); 
+      double nc_ll = (result[8]); 
+      nu_nc_uu.push_back(nc_ul);
+      nu_nc_lu.push_back(nc_ll);
+      nc_ul/=100.;
+      nc_ll/=100.;
+      nc_ul+=1.; // 1 + upper uncertainty on nc (result[6]>0)
+      nc_ll+=1.; // 1 + lower uncertainty on nc (result[8]<0)
+      nu_nc_ul.push_back(result[5]*nc_ul);
+      nu_nc_ll.push_back(result[5]*nc_ll);
+    }
+  }
+  fin_nu.close();
+
+  // for(int i=0; i<energy.size(); i++){
+  //  printf("Energy %e, sigma %e, err+ %.2f, err- %.2f \n", energy[i], nu_cc[i], nu_cc_ul[i], nu_cc_ll[i]);
+  // }
+  // cout<<""<<endl;
+
+  // then, load the anti-neutrino (nubar) cross sections
+  ifstream fin_nubar("./data/coopersarkar_sigma_nubar.csv");
+  if(fin_nubar.is_open()){
+    while(fin_nubar.good()){
+      getline(fin_nubar, line);
+      stringstream s_stream(line);
+      vector<double> result;
+      while(s_stream.good()){
+        string substr;
+        getline(s_stream, substr, ',');
+        result.push_back(atof(substr.c_str()));
+      }
+      nubar_cc.push_back(result[1]); // charged current cross-section
+      double cc_ul = (result[2]); 
+      double cc_ll = (result[4]); 
+      nubar_cc_uu.push_back(cc_ul);
+      nubar_cc_lu.push_back(cc_ll);
+      cc_ul/=100.; // convert from % to fraction
+      cc_ll/=100.; // convert from % to fraction
+      cc_ul+=1.; // 1 + upper uncertainty on cc (result[2]>0)
+      cc_ll+=1.; // 1 + lower uncertainty on cc (result[4]<0)
+      nubar_cc_ul.push_back(result[1]*cc_ul);
+      nubar_cc_ll.push_back(result[1]*cc_ll);
+
+      nubar_nc.push_back(result[5]); // neutral current cross-section
+      double nc_ul = (result[6]); 
+      double nc_ll = (result[8]); 
+      nubar_nc_uu.push_back(nc_ul);
+      nubar_nc_lu.push_back(nc_ll);
+      nc_ul/=100.;
+      nc_ll/=100.;
+      nc_ul+=1.; // 1 + upper uncertainty on nc (result[6]>0)
+      nc_ll+=1.; // 1 + lower uncertainty on nc (result[8]<0)
+      nubar_nc_ul.push_back(result[5]*nc_ul);
+      nubar_nc_ll.push_back(result[5]*nc_ll);
+    }
+  }
+  fin_nubar.close();
+
+  // for(int i=0; i<energy.size(); i++){
+  //  printf("Energy %e, sigma %e, err+ %.2f, err- %.2f \n", energy[i], nubar_cc[i], nubar_cc_ul[i], nubar_cc_ll[i]);
+  // }
+  // cout<<""<<endl;
+
+  // go to log-space to do the spline, where we don't have to fit as many orders of magnitude
+  vector<double> logenergy;
+  
+  vector<double> nu_logcc;
+    vector<double> nu_logcc_ul;
+    vector<double> nu_logcc_ll;
+  vector<double> nu_lognc;
+    vector<double> nu_lognc_ul;
+    vector<double> nu_lognc_ll;
+
+  vector<double> nubar_logcc;
+    vector<double> nubar_logcc_ul;
+    vector<double> nubar_logcc_ll;
+  vector<double> nubar_lognc;
+    vector<double> nubar_lognc_ul;
+    vector<double> nubar_lognc_ll;
+  
+  for(int i=0; i<energy.size(); i++){
+    logenergy.push_back(log10(energy[i]));
+    
+    nu_logcc.push_back(log10(nu_cc[i]));
+      nu_logcc_ul.push_back(log10(nu_cc_ul[i]));
+      nu_logcc_ll.push_back(log10(nu_cc_ll[i]));
+    nu_lognc.push_back(log10(nu_nc[i]));
+      nu_lognc_ul.push_back(log10(nu_nc_ul[i]));
+      nu_lognc_ll.push_back(log10(nu_nc_ll[i]));
+    
+
+    nubar_logcc.push_back(log10(nubar_cc[i]));
+      nubar_logcc_ul.push_back(log10(nubar_cc_ul[i]));
+      nubar_logcc_ll.push_back(log10(nubar_cc_ll[i]));
+    nubar_lognc.push_back(log10(nubar_nc[i]));
+      nubar_lognc_ul.push_back(log10(nubar_nc_ul[i]));
+      nubar_lognc_ll.push_back(log10(nubar_nc_ll[i]));
+  }
+
+  /*
+    build a table of objects which have an "Eval" method, 
+    to match what Eugene did for the Connolly et. al result
+    use the TSpline class specifically because it comes with the ROOT histogram library
+    if we had used "standard" ROOT interpolation schemes 
+    e.g. (https://root.cern.ch/function-interpolation)
+    we would have introduced MathMore (and GSL) as requirement to AraSim
+    which we are trying to avoid
+
+
+    first index is nu/nu bar [0][x] = nu, [1][x] = nu-bar
+    second index is nc/cc [x][0] = nc, [x][1] = cc
+  */
+
+  // nu nc
+  cs_fsigma[0][0] = new TSpline3("nu nc", &logenergy[0], &nu_lognc[0], logenergy.size());
+    cs_fsigma_upper[0][0] = new TSpline3("nu nc ul", &logenergy[0], &nu_lognc_ul[0], logenergy.size());
+    cs_fsigma_lower[0][0] = new TSpline3("nu nc ll", &logenergy[0], &nu_lognc_ll[0], logenergy.size());
+    cs_fsigma_uncertainty_upper[0][0] = new TSpline3("nu nc uu", &logenergy[0], &nu_nc_uu[0], logenergy.size());
+    cs_fsigma_uncertainty_lower[0][0] = new TSpline3("nu nc lu", &logenergy[0], &nu_nc_lu[0], logenergy.size());
+  
+  // nu cc
+  cs_fsigma[0][1] = new TSpline3("nu cc", &logenergy[0], &nu_logcc[0], logenergy.size());
+    cs_fsigma_upper[0][1] = new TSpline3("nu cc ul", &logenergy[0], &nu_logcc_ul[0], logenergy.size());
+    cs_fsigma_lower[0][1] = new TSpline3("nu cc ll", &logenergy[0], &nu_logcc_ll[0], logenergy.size());
+    cs_fsigma_uncertainty_upper[0][1] = new TSpline3("nu cc uu", &logenergy[0], &nu_cc_uu[0], logenergy.size());
+    cs_fsigma_uncertainty_lower[0][1] = new TSpline3("nu cc lu", &logenergy[0], &nu_cc_lu[0], logenergy.size());
+
+  // nubar nc
+  cs_fsigma[1][0] = new TSpline3("nubar nc", &logenergy[0], &nubar_lognc[0], logenergy.size());
+    cs_fsigma_upper[1][0] = new TSpline3("nubar nc ul", &logenergy[0], &nubar_lognc_ul[0], logenergy.size());
+    cs_fsigma_lower[1][0] = new TSpline3("nubar nc ll", &logenergy[0], &nubar_lognc_ll[0], logenergy.size());
+    cs_fsigma_uncertainty_upper[1][0] = new TSpline3("nubar nc uu", &logenergy[0], &nubar_nc_uu[0], logenergy.size());
+    cs_fsigma_uncertainty_lower[1][0] = new TSpline3("nubar nc lu", &logenergy[0], &nubar_nc_lu[0], logenergy.size());
+
+  // nubar cc
+  cs_fsigma[1][1] = new TSpline3("nubar cc", &logenergy[0], &nubar_logcc[0], logenergy.size());
+    cs_fsigma_upper[1][1] = new TSpline3("nubar cc ul", &logenergy[0], &nubar_logcc_ul[0], logenergy.size());
+    cs_fsigma_lower[1][1] = new TSpline3("nubar cc ll", &logenergy[0], &nubar_logcc_ll[0], logenergy.size());
+    cs_fsigma_uncertainty_upper[1][1] = new TSpline3("nubar cc uu", &logenergy[0], &nubar_cc_uu[0], logenergy.size());
+    cs_fsigma_uncertainty_lower[1][1] = new TSpline3("nubar cc lu", &logenergy[0], &nubar_cc_lu[0], logenergy.size());
+
   
   run_old_code=0;//for GetSigma() & Gety() runs of the old code if 1, else runs current code.
 
   // 0=Reno
   // 1=Connolly et al. 2011
+  // 2=Cooper-Sarkar et. al. 2011
   mine[0]=1.2E15;
   //mine[1]=1.E4;// minimum energy for cross section parametrizations
   mine[1]=1.E13;// minimum energy for cross section parametrizations
+  mine[2]=5.e10;
   maxe[0]=1.E21;
   maxe[1]=1.E21; // use the same upper limit for reno as for connolly et al.
+  maxe[2]=1.E21; // go up to 1E21, though note these final points are an extrapolation; cooper-sarkar only publish up to 5E20
+
 
 
   // added for air col
@@ -275,8 +475,6 @@ Primaries::Primaries(){//constructor
 
 
 
-
-
 }
 
 Primaries::~Primaries(){//default deconstructor
@@ -398,19 +596,63 @@ int Primaries::GetSigma(double pnu,double& sigma,double &len_int_kgm2,Settings *
           sigma=settings1->SIGMA_FACTOR*(m_fsigma_lower[nu_nubar][currentint]->Eval(epsilon))/1.E4;//convert cm to meters. multiply by (1m^2/10^4 cm^2).
           sigma_total = (settings1->SIGMA_FACTOR*(m_fsigma_lower[nu_nubar][0]->Eval(epsilon))/1.E4) + (settings1->SIGMA_FACTOR*(m_fsigma_lower[nu_nubar][1]->Eval(epsilon))/1.E4);
       }
+      else if (settings1->SIGMA_SELECT==3){ // use Cooper-Sarkar upper uncertainties
+        double cs_uncertainty_this = cs_fsigma_uncertainty_upper[nu_nubar][currentint]->Eval(epsilon);
+        	cs_uncertainty_this/=100.; // change from % to fraction
+        	cs_uncertainty_this+=1.; // turn it into a multiplicative factor
+        double cs_uncertainty_nc = cs_fsigma_uncertainty_upper[nu_nubar][0]->Eval(epsilon);
+        	cs_uncertainty_nc/=100.;
+       	 cs_uncertainty_nc+=1.;
+        double cs_uncertainty_cc = cs_fsigma_uncertainty_upper[nu_nubar][1]->Eval(epsilon);
+        	cs_uncertainty_cc/=100.;
+        	cs_uncertainty_cc+=1.;
+        sigma=settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][currentint]->Eval(epsilon))/1.E4*cs_uncertainty_this ;//convert cm to meters. multiply by (1m^2/10^4 cm^2).
+        sigma_total = (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][0]->Eval(epsilon))/1.E4*cs_uncertainty_nc) + (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][1]->Eval(epsilon))/1.E4*cs_uncertainty_cc);
+      }
+      else if(settings1->SIGMA_SELECT==4){ // use Cooper-Sarkar lower uncertainties
+        double cs_uncertainty_this = cs_fsigma_uncertainty_lower[nu_nubar][currentint]->Eval(epsilon);
+        	cs_uncertainty_this/=100.; // change from % to fraction
+        	cs_uncertainty_this+=1.; // turn it into a multiplicative factor
+        double cs_uncertainty_nc = cs_fsigma_uncertainty_lower[nu_nubar][0]->Eval(epsilon);
+        	cs_uncertainty_nc/=100.;
+        	cs_uncertainty_nc+=1.;
+        double cs_uncertainty_cc = cs_fsigma_uncertainty_lower[nu_nubar][1]->Eval(epsilon);
+        	cs_uncertainty_cc/=100.;
+        	cs_uncertainty_cc+=1.;
+        sigma=settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][currentint]->Eval(epsilon))/1.E4*cs_uncertainty_this ;//convert cm to meters. multiply by (1m^2/10^4 cm^2).
+        sigma_total = (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][0]->Eval(epsilon))/1.E4*cs_uncertainty_nc) + (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][1]->Eval(epsilon))/1.E4*cs_uncertainty_cc);
+      }
       else {// if other values are chosen, just use mean value
 
           sigma=settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][currentint]->Eval(epsilon))/1.E4;//convert cm to meters. multiply by (1m^2/10^4 cm^2).
           sigma_total = (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][0]->Eval(epsilon))/1.E4) + (settings1->SIGMA_FACTOR*(m_fsigma[nu_nubar][1]->Eval(epsilon))/1.E4);
-      }
-
-
-      
+      }   
       if(m_hsigma->GetEntries()<2000){
-	m_hsigma->Fill(epsilon, log10(sigma));
+	     m_hsigma->Fill(epsilon, log10(sigma));
       }
     }//else current code
+    else if(settings1->SIGMAPARAM==2){//Cooper-Sarkar et al.
+      double pnuGeV=pnu/1.E9;
+      double epsilon=log10(pnuGeV);
+      if(settings1->SIGMA_SELECT==0){// use mean value
+        sigma=settings1->SIGMA_FACTOR*(pow(10.,cs_fsigma[nu_nubar][currentint]->Eval(epsilon)))/1.E40; //convert picobarns to m^2
+        sigma_total = (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma[nu_nubar][0]->Eval(epsilon)))/1.E40) + (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma[nu_nubar][1]->Eval(epsilon)))/1.E40);
+      }
+      else if(settings1->SIGMA_SELECT==1){// use upper bound value
+        sigma=settings1->SIGMA_FACTOR*(pow(10.,cs_fsigma_upper[nu_nubar][currentint]->Eval(epsilon)))/1.E40; //convert picobarns to m^2
+        sigma_total = (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma_upper[nu_nubar][0]->Eval(epsilon)))/1.E40) + (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma_upper[nu_nubar][1]->Eval(epsilon)))/1.E40);
+      }
+      else if(settings1->SIGMA_SELECT==1){// use lower bound value
+        sigma=settings1->SIGMA_FACTOR*(pow(10.,cs_fsigma_lower[nu_nubar][currentint]->Eval(epsilon)))/1.E40; //convert picobarns to m^2
+        sigma_total = (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma_lower[nu_nubar][0]->Eval(epsilon)))/1.E40) + (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma_lower[nu_nubar][1]->Eval(epsilon)))/1.E40);
+      }
+      else{// if other values are chosen, just use mean value
+        sigma=settings1->SIGMA_FACTOR*(pow(10.,cs_fsigma[nu_nubar][currentint]->Eval(epsilon)))/1.0E40; //convert picobarns to m^2
+        sigma_total = (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma[nu_nubar][0]->Eval(epsilon)))/1.E40) + (settings1->SIGMA_FACTOR*(pow(10.,m_fsigma[nu_nubar][1]->Eval(epsilon)))/1.E40);
+      }
+    }
   }//if
+
   // interaction length in kg/m^2
   
   len_int_kgm2=M_NUCL/sigma; // kg/m^2
diff --git a/Primaries.h b/Primaries.h
index 8e9a371c..f952395c 100644
--- a/Primaries.h
+++ b/Primaries.h
@@ -19,6 +19,7 @@
 #include "Vector.h"
 #include <vector>
 #include "Position.h"
+#include "TSpline.h"
 
 //--------------------------------------------------
 // class Interaction;
@@ -125,10 +126,19 @@ class Primaries {
 	double c3_lower[2][2];
 	double c4_lower[2][2];
 
+  // cooper sarkar
+  // first index is nu/nu bar [0][x] = nu, [1][x] = nu-bar
+  // second index is nc/cc [x][0] = nc, [x][1] = cc
+  TSpline3* cs_fsigma[2][2]; // spline for cooper-sarkar central sigma values
+  TSpline3* cs_fsigma_upper[2][2]; // spline for cooper-sarkar upper limit sigma values
+  TSpline3* cs_fsigma_lower[2][2]; // spline for cooper-sarkar lower limit sigma values
+  TSpline3* cs_fsigma_uncertainty_upper[2][2]; // the *relative* [%] upper uncertainties
+  TSpline3* cs_fsigma_uncertainty_lower[2][2]; // the rrelative* [%] lower uncertainties
 
-	static const int NSIGMAS=2;// number of possible cross section models
+	static const int NSIGMAS=3;// number of possible cross section models
 	// 0=Gandhi et al.
 	// 1=Connolly et al. 2011
+  // 2=Cooper-Sarkar et. al. 2011 (https://arxiv.org/abs/1106.3723)
 	double mine[NSIGMAS];// minimum energy for cross section parametrizations, in eV
 	double maxe[NSIGMAS]; //max
 
diff --git a/RaySolver.cc b/RaySolver.cc
index 0e5bb847..2e86a3d3 100644
--- a/RaySolver.cc
+++ b/RaySolver.cc
@@ -1076,12 +1076,38 @@ void RaySolver::Solve_Ray (Position &source, Position &target, IceModel *antarct
     // Defaults!!!!
     src = source_tmp;
     trg = target_tmp;
-    
+
     if (settings1->RAY_TRACE_ICE_MODEL_PARAMS == 0){
     // South Pole Values (AraSim original default, based on RICE)
       ns = 1.35;
       nd = 1.78;
       nc = 0.0132;
+
+      // printf("Old ns, nd, nc: %.4f, %.4f, %.4f \n", ns, nd, nc);
+
+      // if we wan to wiggle parameter uncertaintties
+      double adjust_ns=0.;
+      double adjust_nd=0.;
+      double adjust_nc=0.;
+
+      if(settings1->SYSTEMATICS_nofz==1){ // upper bound
+        adjust_ns=0.022;
+        adjust_nd=0.016;
+        adjust_nc=0.0017;
+      }
+      if(settings1->SYSTEMATICS_nofz==2){ // lower bound
+        adjust_ns=-0.022;
+        adjust_nd=-0.016;
+        adjust_nc=-0.0017;
+      }
+
+      ns+=adjust_ns;
+      nd+=adjust_nd;
+      nc+=adjust_nc;
+
+      // printf("New ns, nd, nc: %.4f, %.4f, %.4f \n", ns, nd, nc);
+
+
     } else if (settings1->RAY_TRACE_ICE_MODEL_PARAMS == 1){
       // South Pole Values (RICE (2004))
       ns = 1.35;
@@ -1123,10 +1149,7 @@ void RaySolver::Solve_Ray (Position &source, Position &target, IceModel *antarct
       ns = 1.35;
       nd = 1.78;
       nc = 0.0132;
-    } 
-
-
-
+    }
 
 
     //    cout << "ns, nd, nc: " << ns << ", " << nd << ", " << nc << endl;
diff --git a/Report.cc b/Report.cc
index 02d03e30..6891d090 100644
--- a/Report.cc
+++ b/Report.cc
@@ -34,7 +34,7 @@ Report::Report(Detector *detector, Settings *settings1) {
     // Default constructor
 
     Initialize(detector, settings1);
-    
+
 }
 
 
@@ -71,7 +71,7 @@ void Report::delete_all() {
 }
 
 void Report::Initialize(Detector *detector, Settings *settings1) {
-    
+
     // clear information stored in (but there shouldn't be. just to make sure)
     //
     //stations.clear();
@@ -102,23 +102,23 @@ void Report::Initialize(Detector *detector, Settings *settings1) {
 
 	if(settings1->TRIG_SCAN_MODE>0){// scan Pthresh mode
 
-	  int numChan=0; 
+	  int numChan=0;
 	  int numChanVpol=0;
 	  int numChanHpol=0;
-	  
+
 	  for(int j=0;j<detector->stations[i].strings.size(); j++){
-	    
+
 	    for (int k=0;k<detector->stations[i].strings[j].antennas.size();k++) {
-	      
+
 	      int string_i = detector->getStringfromArbAntID( i, numChan);
               int antenna_i = detector->getAntennafromArbAntID( i, numChan);
 	      if (detector->stations[i].strings[string_i].antennas[antenna_i].type == 0) numChanVpol++;
 	      if (detector->stations[i].strings[string_i].antennas[antenna_i].type == 1) numChanHpol++;
 	      numChan++;
 	    }// for k
-	    
+
 	  }// for j
-	  
+
 	  stations[i].TDR_all.clear();
 	  for(int ch=0;ch<numChan; ch++ ) stations[i].TDR_all.push_back(0);
 	  stations[i].TDR_all_sorted.clear();
@@ -130,9 +130,9 @@ void Report::Initialize(Detector *detector, Settings *settings1) {
 	  stations[i].TDR_Hpol_sorted.clear();
 	  if(settings1->TRIG_MODE==1) for(int ch=0;ch<numChanHpol; ch++ ) stations[i].TDR_Hpol_sorted.push_back(0);
 
-	  
-	}// if TRIG_SCAN_MODE 
-	
+
+	}// if TRIG_SCAN_MODE
+
     }// for i (number of stations)
 
 
@@ -143,7 +143,7 @@ void Report::Initialize(Detector *detector, Settings *settings1) {
 
 
 void Antenna_r::clear() {   // if any vector variable added in Antenna_r, need to be added here!
-    
+
     view_ang.clear();
     launch_ang.clear();
     rec_ang.clear();
@@ -191,10 +191,10 @@ void Antenna_r::clear() {   // if any vector variable added in Antenna_r, need t
     Vm_zoom_T.clear();
 
     SignalBin.clear();
-    SignalExt.clear(); 
-    
+    SignalExt.clear();
+
     SCT_threshold_pass.clear();
-    
+
 }
 
 
@@ -204,7 +204,7 @@ void Antenna_r::clear_useless(Settings *settings1) {   // to reduce the size of
 
     if (settings1->DATA_SAVE_MODE == 1) {
     Heff.clear();
-    
+
     //VHz_antfactor.clear();
     //VHz_filter.clear();
     Vfft.clear();
@@ -237,8 +237,8 @@ void Antenna_r::clear_useless(Settings *settings1) {   // to reduce the size of
 
     }
     else if (settings1->DATA_SAVE_MODE == 2) {
-      
-    
+
+
     Heff.clear();
     //VHz_antfactor.clear();
     //VHz_filter.clear();
@@ -264,7 +264,7 @@ void Antenna_r::clear_useless(Settings *settings1) {   // to reduce the size of
     //Mag.clear();
     //Fresnel.clear();
     //Pol_factor.clear();
-    
+
     // clear global trigger waveform info also
     time.clear();
     time_mimic.clear();
@@ -275,7 +275,7 @@ void Antenna_r::clear_useless(Settings *settings1) {   // to reduce the size of
     //Vm_wo_antfactor.clear();
     Vm_zoom.clear();
     Vm_zoom_T.clear();
-    
+
     }
 
 
@@ -300,7 +300,7 @@ void Report::clear_useless(Settings *settings1) {   // to reduce the size of out
         //V_noise_timedomain.clear();
         // done clear vector info in report head
         //
-    
+
         V_total_forconvlv.clear();
 	RayStep.clear();
 
@@ -345,7 +345,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
     int waveformLength = settings1->WAVEFORM_LENGTH;
     int waveformCenter = settings1->WAVEFORM_CENTER;
-			       
+
 
     //double dF_outbin;
     double dF_Nnew;
@@ -378,63 +378,63 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
     //else if ( settings1->DEBUG_MODE_ON == 1 && evt >= settings1->DEBUG_SKIP_EVT ) cout<<"After DEBUG_SKIP_EVT"<<endl;
     else if ( settings1->DEBUG_MODE_ON == 1 && evt >= settings1->DEBUG_SKIP_EVT ) cout<<evt<<" "<<endl;
     // skip most of computation intensive processes if debugmode == 1
-    
-    
+
+
     int N_pass; // number of trigger passed channels (antennas)
     int N_pass_V; // number of trigger passed channels (Vpol antennas)
     int N_pass_H; // number of trigger passed channels (Hpol antennas)
 
     for (int i = 0; i< detector->params.number_of_stations; i++) {
-      
+
       min_arrival_time_tmp = 10.;      // first min_arrival_time is unreasonably big value
       max_arrival_time_tmp = 0.;      // first max_arrival_time is unreasonably small value
       max_PeakV_tmp = 0.;  // first max_PeakV_tmp is 0.
-      
+
       stations[i].Total_ray_sol=0; // initial Total_ray_sol value
-      
-      
-      
+
+
+
       for (int j=0; j< detector->stations[i].strings.size(); j++) {
-	
+
 	for (int k=0; k< detector->stations[i].strings[j].antennas.size(); k++) {
 	  //	  cout << i << " : " << j << " : " << k << endl;
-	  
+
 	  stations[i].strings[j].antennas[k].clear();  // clear data in antenna which stored in previous event
-	  
+
 	  // run ray solver, see if solution exist
 	  // if not, skip (set something like Sol_No = 0;
 	  // if solution exist, calculate view angle and calculate TaperVmMHz
-	  
+
 	  // added one more condition to run raysolver ( direct distance is less than 3km )
 	  //
 
 	  //	  cout << event->Nu_Interaction[0].posnu.GetX() << " : " << event->Nu_Interaction[0].posnu.GetY() << " : " << event->Nu_Interaction[0].posnu.GetZ() << endl;
-	  //	  cout << event->Nu_Interaction[0].pickposnu << " : " << event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[j].antennas[k] ) << " : " << settings1->RAYSOL_RANGE << endl; 
+	  //	  cout << event->Nu_Interaction[0].pickposnu << " : " << event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[j].antennas[k] ) << " : " << settings1->RAYSOL_RANGE << endl;
 	  if (event->Nu_Interaction[0].pickposnu && event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[j].antennas[k] ) <= settings1->RAYSOL_RANGE ) {    // if posnu is selected inside the antarctic ic:"<<viewangle<<" th_em:"<<d_theta_em[l]<<" th_had:"<<d_theta_had[l]<<" emfrac:"<<emfrac<<" hadfrac:"<<hadfrac<<" vmmhz1m:"<<vmmhz1m[l]<<endl;e
 	    //if (event->Nu_Interaction[0].pickposnu && event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[j].antennas[k] ) <= settings1->RAYSOL_RANGE && debugmode == 0 ) {    // if posnu is selected inside the antarctic ic:"<<viewangle<<" th_em:"<<d_theta_em[l]<<" th_had:"<<d_theta_had[l]<<" emfrac:"<<emfrac<<" hadfrac:"<<hadfrac<<" vmmhz1m:"<<vmmhz1m[l]<<endl;e
 	    //cout << i << " : " << j << " : " << k << endl;
-            
+
 	    //raysolver->Solve_Ray(event->Nu_Interaction[0].posnu, detector->stations[i].strings[j].antennas[k], icemodel, ray_output, settings1);   // solve ray between source and antenna
 	    RayStep.clear(); // remove previous values
 	    raysolver->Solve_Ray(event->Nu_Interaction[0].posnu, detector->stations[i].strings[j].antennas[k], icemodel, ray_output, settings1, RayStep);   // solve ray between source and antenna
-            
+
 	    ray_sol_cnt = 0;
-            
+
 	    if (raysolver->solution_toggle) {  // if there are solution from raysolver
 	      //if (raysolver->solution_toggle && debugmode==0 ) {  // if there are solution from raysolver
-              
-	      
+
+
 	      while ( ray_sol_cnt < ray_output[0].size() ) {   // for number of soultions (could be 1 or 2)
-		
-		
+
+
 		stations[i].strings[j].antennas[k].arrival_time.push_back(ray_output[4][ray_sol_cnt]);
-		
-		
+
+
 		// get ice attenuation factor
 		//
-                                   double IceAttenFactor = 1.; 
+                                   double IceAttenFactor = 1.;
                                    if ( settings1->USE_ARA_ICEATTENU==1 ) {// use new ARA measured ice attenuation values
-				     
+
 				     double dx, dz, dl;
 				     for (int steps=1; steps<(int)RayStep[ray_sol_cnt][0].size(); steps++) {
 
@@ -448,7 +448,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                        //cout<<"new iceattenfactor : "<<IceAttenFactor<<", old way : "<<exp(-ray_output[0][ray_sol_cnt]/icemodel->EffectiveAttenuationLength(settings1, event->Nu_Interaction[0].posnu, 0))<<endl;
                                    }
                                    else if ( settings1->USE_ARA_ICEATTENU==0 ) {// use old method
-                                          
+
                                        IceAttenFactor = exp(-ray_output[0][ray_sol_cnt]/icemodel->EffectiveAttenuationLength(settings1, event->Nu_Interaction[0].posnu, 0));
                                    }
 
@@ -487,11 +487,11 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                    stations[i].strings[j].antennas[k].L_att.push_back( icemodel->EffectiveAttenuationLength(settings1, event->Nu_Interaction[0].posnu, 0) );
                                    //stations[i].strings[j].antennas[k].arrival_time.push_back(ray_output[4][ray_sol_cnt]);
                                    stations[i].strings[j].antennas[k].reflect_ang.push_back(ray_output[3][ray_sol_cnt]);
-                                   
+
                                    stations[i].strings[j].antennas[k].vmmhz.resize(ray_sol_cnt+1);
 
                                    stations[i].strings[j].antennas[k].Heff.resize(ray_sol_cnt+1);
-                                   
+
                                    stations[i].strings[j].antennas[k].Vm_zoom.resize(ray_sol_cnt+1);
                                    stations[i].strings[j].antennas[k].Vm_zoom_T.resize(ray_sol_cnt+1);
 
@@ -547,7 +547,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                                    GetAngleAnt(receive_vector, detector->stations[i].strings[j].antennas[k], antenna_theta, antenna_phi);   // get theta, phi for signal ray arrived at antenna
-                                   //cout<<"antenna theta : "<<antenna_theta<<"  phi : "<<antenna_phi<<endl;  
+                                   //cout<<"antenna theta : "<<antenna_theta<<"  phi : "<<antenna_phi<<endl;
 
 
 
@@ -564,7 +564,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                        for (int l=0; l<detector->GetFreqBin(); l++) {   // for detector freq bin numbers
 
-                                        
+
                                           //cout<<"TaperVmMHz inputs VA:"<<viewangle<<" th_em:"<<event->Nu_Interaction[0].d_theta_em[l]<<" th_had:"<<event->Nu_Interaction[0].d_theta_had[l]<<" emfrac:"<<event->Nu_Interaction[0].emfrac<<" hadfrac:"<<event->Nu_Interaction[0].hadfrac<<" vmmhz1m:"<<event->Nu_Interaction[0].vmmhz1m[l]<<endl;
     //                                       switch (event->IsCalpulser){
     //                                           case 0:
@@ -576,8 +576,8 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                                vmmhz1m_tmp = event->Nu_Interaction[0].vmmhz1m[l];
                                                signal->TaperVmMHz( viewangle, event->Nu_Interaction[0].d_theta_em[l], event->Nu_Interaction[0].d_theta_had[l], event->Nu_Interaction[0].emfrac, event->Nu_Interaction[0].hadfrac, vmmhz1m_tmp, vmmhz1m_em);
                                            }
-                                           
-                                           
+
+
     //                                               break;
     //                                           case 1:
     //                                               vmmhz1m_tmp = 0;
@@ -589,9 +589,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
     //                                               vmmhz1m_tmp = event->Nu_Interaction[0].vmmhz1m[l];
     //                                               break;
     //                                       }
-                                           
-                                           
-                                           
+
+
+
     //                                       signal->TaperVmMHz( viewangle, event->Nu_Interaction[0].d_theta_em[l], event->Nu_Interaction[0].d_theta_had[l], event->Nu_Interaction[0].emfrac, event->Nu_Interaction[0].hadfrac, vmmhz1m_tmp, vmmhz1m_em);
                                           //cout<<"TaperVmMHz (1m at view angle) at "<<l<<"th bin : "<<vmmhz1m_tmp<<endl;
 
@@ -612,33 +612,33 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 					   cout << "Check 1" << endl;
                                            /*
-                                           // Get ant gain with 2-D interpolation (may have bug?) 
+                                           // Get ant gain with 2-D interpolation (may have bug?)
                                            //
                                            heff = GaintoHeight(detector->stations[i].strings[j].antennas[k].GetG(detector, freq_tmp*1.E-6, // to MHz
-                                                       antenna_theta, antenna_phi), 
+                                                       antenna_theta, antenna_phi),
                                                        freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
                                             */
                                            if ( settings1->ALL_ANT_V_ON==0 ) {
 					     if (settings1->ANTENNA_MODE == 0){
                                                heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
                                                            freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
 					       heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
                                            }
                                            else if ( settings1->ALL_ANT_V_ON==1 ) {
 					     if (settings1->ANTENNA_MODE == 0){
                                                heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, 0), 
+												antenna_theta, antenna_phi, 0),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
                                                heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, 0, k), 
+												antenna_theta, antenna_phi, 0, k),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					   }
@@ -665,7 +665,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                                //cout<<"set signal pol as Vpol + Hpol for Calpulser2 evts"<<endl;
                                                Pol_vector = n_trg_slappy + n_trg_pokey;
                                            }
-                                           
+
                                            ApplyAntFactors(heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, vmmhz1m_tmp);
 
 					   cout << "Check 2" << endl;
@@ -687,7 +687,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                                        }// end for freq bin
-                                       
+
                                        stations[i].strings[j].antennas[k].Pol_factor.push_back( Pol_factor );
 
 
@@ -712,13 +712,13 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                                        //cout<<"Finished getting V signal part!!"<<endl;
-                                       
+
                                        stations[i].strings[j].antennas[k].PeakV.push_back( FindPeak(volts_forfft, settings1->NFOUR/2) );
 
                                        // Vfft_noise_org is in fft freq bin!!
                                        // same unit with Vfft [V] but filter not applied
 
-                                       
+
                                        Tools::NormalTimeOrdering(settings1->NFOUR/2, volts_forfft);
                                        //cout<<"finished NormalTimeOrdering!!"<<endl;
 
@@ -743,7 +743,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
 
-                                               
+
                                        // if event is not calpulser
                                        if (event->IsCalpulser == 0){
 
@@ -758,7 +758,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                                // initially give raysol has actual signal
                                                stations[i].strings[j].antennas[k].SignalExt[ray_sol_cnt] = 1;
 
-                                               
+
 
                                                // let's make NFOUR/2 bin of time domain pure signal part for now
                                                // later once we understand how to apply antenna phase, total electronics with phase, apply those
@@ -769,10 +769,22 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                                // signal before the antenna (get signal at 1m and apply atten factor)
                                                signal->GetVm_FarField_Tarray( event, settings1, viewangle, atten_factor, outbin, Tarray, Earray, stations[i].strings[j].antennas[k].skip_bins[ray_sol_cnt] );
+                                               // cout << "\033[1;31mAskaryan Signal accessed here\033[0m\n";
+					                                       if(settings1->SYSTEMATICS_Askaryan>0){
+                                                   if(settings1->SYSTEMATICS_Askaryan==1) for(int kk=0;kk<64;kk++){
+                                                     // printf("Before:%e \n",Earray[kk]);
+                                                     Earray[kk]*=1.12;
+                                                     // printf("After:%e \n",Earray[kk]);
+                                                   }
+                                                   if(settings1->SYSTEMATICS_Askaryan==2) for(int kk=0;kk<64;kk++){
+                                                     // printf("Before:%e \n",Earray[kk]);
+                                                     Earray[kk]*=0.88;
+                                                     // printf("After:%e \n",Earray[kk]);
+                                                   }
+                                               }
 
 
 
-                                           
                                                dT_forfft = Tarray[1] - Tarray[0]; // step in ns
 
                                                int Ntmp = settings1->TIMESTEP*1.e9 / dT_forfft;
@@ -814,7 +826,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                                    else
                                                        V_forfft[n] = 0.;
 
-                                                     
+
 
                                                    //stations[i].strings[j].antennas[k].Vm_wo_antfactor[ray_sol_cnt].push_back( V_forfft[n] );
 
@@ -856,37 +868,37 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                                                /*
-                                               // Get ant gain with 2-D interpolation (may have bug?) 
+                                               // Get ant gain with 2-D interpolation (may have bug?)
                                                //
                                                heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-                                                           antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+                                                           antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
                                                            freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
                                                 */
                                                if ( settings1->ALL_ANT_V_ON==0 ) {
 						 if (settings1->ANTENNA_MODE == 0){
                                                    heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-                                                               antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+                                                               antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
                                                                freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						 }
 						 if (settings1->ANTENNA_MODE == 1){
                                                    heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+													    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
                                                                freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						 }
                                                }
                                                else if ( settings1->ALL_ANT_V_ON==1 ) {
-                                                   
+
 						 if (settings1->ANTENNA_MODE == 0){
 						   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													    antenna_theta, antenna_phi, 0), 
+													    antenna_theta, antenna_phi, 0),
 									       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						 }
 						 if (settings1->ANTENNA_MODE == 1){
 						   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													    antenna_theta, antenna_phi, 0, k), 
+													    antenna_theta, antenna_phi, 0, k),
 									       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						 }
-						 
+
 
 
                                                }
@@ -903,31 +915,31 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                                    /*
                                                    heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-                                                               antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+                                                               antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
                                                                freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
                                                     */
                                                    if ( settings1->ALL_ANT_V_ON==0 ) {
 						     if (settings1->ANTENNA_MODE == 0){
                                                        heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+													antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 									   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						     }
-        
+
 						     if (settings1->ANTENNA_MODE == 1){
                                                        heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+													antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
 									   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						     }
                                                    }
                                                    else if ( settings1->ALL_ANT_V_ON==1 ) {
 						     if (settings1->ANTENNA_MODE == 0){
                                                        heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-                                                                   antenna_theta, antenna_phi, 0), 
+                                                                   antenna_theta, antenna_phi, 0),
                                                                    freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						     }
 						     if (settings1->ANTENNA_MODE == 1){
                                                        heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													antenna_theta, antenna_phi, 0, k), 
+													antenna_theta, antenna_phi, 0, k),
 									   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 						     }
                                                    }
@@ -945,7 +957,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                                    if ( n > 0 ) {
 
                                                        if ( settings1->ALL_ANT_V_ON==0 ) {
-                                                       
+
                                                            ApplyAntFactors_Tdomain( detector->GetAntPhase_1D( freq_tmp*1.e-6, antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type ),
                                                                heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
                                                        }
@@ -1045,11 +1057,11 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 					 // initially give raysol has actual signal
 					 stations[i].strings[j].antennas[k].SignalExt[ray_sol_cnt] = 1;
-					 
+
 
 					 int waveform_bin = (int)signal->ArbitraryWaveform_V.size();
 					 //					 cout << waveform_bin << endl;
-					 
+
 					 //dT_forfft = Tarray[1] - Tarray[0]; // step in ns
 					 //dT_forfft = detector->CalPulserWF_ns[1] - detector->CalPulserWF_ns[0]; // step in ns
 					 dT_forfft = signal->ArbitraryWaveform_T[1]-signal->ArbitraryWaveform_T[0]; // step in ns
@@ -1065,17 +1077,17 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					 }
 					 stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] = stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] * settings1->NFOUR/2;
 					 // now new NFOUR for zero padding
-					 
-					 
-					 
+
+
+
 					 // now we have to make NFOUR/2 number of bins with random init time
 					 //
 					 // as a test, make first as it is and zero pad
-					 
-					 
+
+
 					 double V_forfft[ stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] ];
 					 double T_forfft[ stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] ];
-					 
+
 					 for (int n=0; n<stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]; n++) {
 					   //cout << n << endl;
 					   if ( n<waveform_bin ) {
@@ -1083,46 +1095,46 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					     stations[i].strings[j].antennas[k].Vm_zoom_T[ray_sol_cnt].push_back( signal->ArbitraryWaveform_T[n] );
 					     //cout << signal->ArbitraryWaveform_T[n] << " : " << signal->ArbitraryWaveform_V[n] << endl;
 					   }
-					   
+
 					   // make Tarray, Earray located at the center of Nnew array
 					   //T_forfft[n] = Tarray[outbin/2] - (dT_forfft*(double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2)) + (double)n*dT_forfft;
-					   
+
 					   T_forfft[n] = signal->ArbitraryWaveform_T[waveform_bin/2] - (dT_forfft*(double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - n));
-					   
+
 					   if ( (n >= stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - waveform_bin/2) &&
 						(n < stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 + waveform_bin/2) ) {
 					     V_forfft[n] = signal->ArbitraryWaveform_V[ n - (stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - waveform_bin/2) ];
-					   
+
 					   }					   else
 					     V_forfft[n] = 0.;
-					   
-                                           
-					   
+
+
+
 					   //stations[i].strings[j].antennas[k].Vm_wo_antfactor[ray_sol_cnt].push_back( V_forfft[n] );
-					   
+
 					 }
-					 
 
-					 
+
+
 					 // just get peak from the array
 					 //stations[i].strings[j].antennas[k].PeakV.push_back( FindPeak(detector->CalPulserWF_V, CP_bin) );
 					 stations[i].strings[j].antennas[k].PeakV.push_back( -1. );// just let -1.
-					 
-					 
+
+
 					 // get spectrum with zero padded WF
 					 //Tools::realft(volts_forfft,1,settings1->NFOUR/2);
 					 Tools::realft(V_forfft,1,stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]);
-					 
+
 					 //dF_outbin = 1./( (double)(outbin) * (Tarray[1]-Tarray[0])*1.e-9 ); // in Hz
 					 dF_Nnew = 1./( (double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]) * (dT_forfft)*1.e-9 ); // in Hz
-					 
+
 					 //freq_tmp = dF_Nnew*((double)stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2.+1.+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
 					 freq_tmp = dF_Nnew*((double)stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2.+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
-					 
+
 					 freq_lastbin = freq_tmp;
-					 
 
-					 
+
+
 					 /*
 					 // heff last bin for transmitter ant
 					 double heff_lastbin_trans;
@@ -1130,47 +1142,47 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					 //cout<<"ant theta trans : "<<ant_theta_trans<<"deg"<<endl;
 					 if ( settings1->ALL_ANT_V_ON==0 ) {
 					   heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													  ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+													  ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 									     freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					 }
 					 else if ( settings1->ALL_ANT_V_ON==1 ) {
 					   heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													  ant_theta_trans, antenna_phi, 0), 
+													  ant_theta_trans, antenna_phi, 0),
 									     freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					 }
-					 
-					 
-					 
-					 
+
+
+
+
 					 // heff last bin for receiver ant
 					 /*
-					 // Get ant gain with 2-D interpolation (may have bug?) 
+					 // Get ant gain with 2-D interpolation (may have bug?)
 					 //
 					 heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-					 antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+					 antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 					 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 */
-					 /*					 
+					 /*
 					 if ( settings1->ALL_ANT_V_ON==0 ) {
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 }
 					 else if ( settings1->ALL_ANT_V_ON==1 ) {
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, 0), 
+												    antenna_theta, antenna_phi, 0),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 }
-					 */					 
+					 */
 					 // Pol_vector = n_trg_slappy;
-					 Pol_vector = n_trg_pokey;					 
-					 
-					 
+					 Pol_vector = n_trg_pokey;
+
+
 					 //
 					 //
 					 for (int n=0; n<stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2; n++) {
-					   
-					   
+
+
 					   freq_tmp = dF_Nnew*((double)n+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
 					   /*
 					   //
@@ -1178,19 +1190,19 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   //
 					   if ( settings1->ALL_ANT_V_ON==0 ) {
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					   else if ( settings1->ALL_ANT_V_ON==1 ) {
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, 0), 
+											      ant_theta_trans, antenna_phi, 0),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					   //
 					   if ( n > 0 ) {
-					     
+
 					     if ( settings1->ALL_ANT_V_ON==0 ) {
-					       
+
 					       ApplyAntFactors_Tdomain_Transmitter( detector->GetAntPhase_1D( freq_tmp*1.e-6, ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type ),
 										    heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
@@ -1198,32 +1210,32 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					       ApplyAntFactors_Tdomain_Transmitter( detector->GetAntPhase_1D( freq_tmp*1.e-6, ant_theta_trans, antenna_phi, 0 ),
 										    heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
-					     
-					     
-					     
+
+
+
 					   }
 					   else {
 					     ApplyAntFactors_Tdomain_FirstTwo( heff, heff_lastbin_trans, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
+
 					   //
 					   // apply ant factors (receiver ant)
 					   //
 					   /*
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-					     antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+					     antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 					     freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					   */
-					 
+
 					   if ( settings1->ALL_ANT_V_ON==0 ) {
 					     if (settings1->ANTENNA_MODE == 0){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
 					       heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type,k), 
+												antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type,k),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					   }
@@ -1231,25 +1243,25 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   else if ( settings1->ALL_ANT_V_ON==1 ) {
 					     if (settings1->ANTENNA_MODE == 0){
 					       heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, 0), 
+												antenna_theta, antenna_phi, 0),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
 					       heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												antenna_theta, antenna_phi, 0,k), 
+												antenna_theta, antenna_phi, 0,k),
 								   freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
-					       
-					     }					
+
+					     }
 					   }
-					   
+
 					   stations[i].strings[j].antennas[k].Heff[ray_sol_cnt].push_back( heff );
-					   
-					   
+
+
 					   if ( n > 0 ) {
-					     
+
 					     if ( settings1->ALL_ANT_V_ON==0 ) {
-					       
+
 					       ApplyAntFactors_Tdomain( detector->GetAntPhase_1D( freq_tmp*1.e-6, antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type ),
 									heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
@@ -1257,14 +1269,14 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					       ApplyAntFactors_Tdomain( detector->GetAntPhase_1D( freq_tmp*1.e-6, antenna_theta, antenna_phi, 0 ),
 									heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
-					     
-					     
-					     
+
+
+
 					   }
 					   else {
 					     ApplyAntFactors_Tdomain_FirstTwo( heff, heff_lastbin, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
+
 					   //
 					   // apply entire elect chain gain, phase
 					   //
@@ -1274,33 +1286,33 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   else {
 					     ApplyElect_Tdomain_FirstTwo( freq_tmp*1.e-6, freq_lastbin*1.e-6, detector, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
-					   
-					   
+
+
+
 					 }// end for freq bin
-					 
+
 
 					 // now get time domain waveform back by inv fft
 					 Tools::realft(V_forfft,-1,stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]);
-					 
-					 
+
+
 					 // we need to do normal time ordering as we did zero padding(?)
 					 // If signal is located at the center, we don't need to do NormalTimeOrdering???
 					 //Tools::NormalTimeOrdering(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt], V_forfft);
-					 
-					 
+
+
 					 // skip linear interpolation for now
 					 Tools::SimpleLinearInterpolation_OutZero( stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt], T_forfft, V_forfft, settings1->NFOUR/2, T_forint, volts_forint );
-					 
+
 					 // check what we save as V[], volts_forint? or volts_forfft
-					 
-					 
-					 
-					 
 
-					 
+
+
+
+
+
 					 for (int n=0; n<settings1->NFOUR/2; n++) {
-					   
+
 					   if (settings1->TRIG_ANALYSIS_MODE != 2) { // not pure noise mode (we need signal)
 					     //stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( volts_forfft[n] );
 					     //stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( V_forfft[n] * 2./(double)(settings1->NFOUR/2) ); // 2/N for inverse FFT normalization factor
@@ -1310,27 +1322,27 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   else if (settings1->TRIG_ANALYSIS_MODE == 2) { // pure noise mode (set signal to 0)
 					     stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( 0. );
 					   }
-					   
+
 					 }
-					 
+
 					 }// Arbitrary Events
 
 
-				       
+
                                        } // if not calpulser event
-                                           
+
                                        // if calpulser event
                                        else if (event->IsCalpulser > 0){
 
 					 // initially give raysol has actual signal
 					 stations[i].strings[j].antennas[k].SignalExt[ray_sol_cnt] = 1;
-					 
+
 					 int CP_bin = (int)detector->CalPulserWF_ns.size();
-					 
-					 
+
+
 					 //dT_forfft = Tarray[1] - Tarray[0]; // step in ns
 					 dT_forfft = detector->CalPulserWF_ns[1] - detector->CalPulserWF_ns[0]; // step in ns
-					 
+
 
 					 int Ntmp = settings1->TIMESTEP*1.e9 / dT_forfft;
 					 stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] = 1;
@@ -1340,65 +1352,65 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					 }
 					 stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] = stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] * settings1->NFOUR/2;
 					 // now new NFOUR for zero padding
-					 
-					 
-					 
+
+
+
 					 // now we have to make NFOUR/2 number of bins with random init time
 					 //
 					 // as a test, make first as it is and zero pad
-					 
-					 
+
+
 					 double V_forfft[ stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] ];
 					 double T_forfft[ stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt] ];
-					 
+
 					 for (int n=0; n<stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]; n++) {
-					   
+
 					   if ( n<CP_bin ) {
 					     stations[i].strings[j].antennas[k].Vm_zoom[ray_sol_cnt].push_back( detector->CalPulserWF_V[n] );
 					     stations[i].strings[j].antennas[k].Vm_zoom_T[ray_sol_cnt].push_back( detector->CalPulserWF_ns[n] );
-					     
+
 					   }
-					   
+
 					   // make Tarray, Earray located at the center of Nnew array
 					   //T_forfft[n] = Tarray[outbin/2] - (dT_forfft*(double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2)) + (double)n*dT_forfft;
-					   
+
 					   T_forfft[n] = detector->CalPulserWF_ns[CP_bin/2] - (dT_forfft*(double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - n));
-					   
+
 					   if ( (n >= stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - CP_bin/2) &&
 						(n < stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 + CP_bin/2) ) {
 					     V_forfft[n] = detector->CalPulserWF_V[ n - (stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2 - CP_bin/2) ];
 					   }
 					   else
 					     V_forfft[n] = 0.;
-					   
-                                           
-					   
+
+
+
 					   //stations[i].strings[j].antennas[k].Vm_wo_antfactor[ray_sol_cnt].push_back( V_forfft[n] );
-					   
+
 					 }
-					 
-					 
-		
+
+
+
 					 // just get peak from the array
 					 //stations[i].strings[j].antennas[k].PeakV.push_back( FindPeak(detector->CalPulserWF_V, CP_bin) );
 					 stations[i].strings[j].antennas[k].PeakV.push_back( -1. );// just let -1.
-					 
-					 
+
+
 					 // get spectrum with zero padded WF
 					 //Tools::realft(volts_forfft,1,settings1->NFOUR/2);
 					 Tools::realft(V_forfft,1,stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]);
-					 
+
 					 //dF_outbin = 1./( (double)(outbin) * (Tarray[1]-Tarray[0])*1.e-9 ); // in Hz
 					 dF_Nnew = 1./( (double)(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]) * (dT_forfft)*1.e-9 ); // in Hz
-					 
+
 					 //freq_tmp = dF_Nnew*((double)stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2.+1.+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
 					 freq_tmp = dF_Nnew*((double)stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2.+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
-					 
+
 					 freq_lastbin = freq_tmp;
-					 
-					 
 
-					 
+
+
+
 					 // heff last bin for transmitter ant
 					 double heff_lastbin_trans;
 					 double ant_theta_trans = ray_output[1][ray_sol_cnt] * DEGRAD; // from 0 to 180
@@ -1406,67 +1418,67 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					 if ( settings1->ALL_ANT_V_ON==0 ) {
 					   if (settings1->ANTENNA_MODE == 0){
 					   heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													  ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+													  ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 									     freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					   if (settings1->ANTENNA_MODE == 1){
 					     heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													    ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+													    ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
 									       freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					 }
 					 else if ( settings1->ALL_ANT_V_ON==1 ) {
 					   if (settings1->ANTENNA_MODE == 0){
 					     heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													  ant_theta_trans, antenna_phi, 0), 
+													  ant_theta_trans, antenna_phi, 0),
 									     freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					   if (settings1->ANTENNA_MODE == 1){
 					     heff_lastbin_trans = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-													    ant_theta_trans, antenna_phi, 0,k), 
+													    ant_theta_trans, antenna_phi, 0,k),
 									     freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					   }
 					 }
-					 
-					 
-					 
-					 
+
+
+
+
 					 // heff last bin for receiver ant
 					 /*
-					 // Get ant gain with 2-D interpolation (may have bug?) 
+					 // Get ant gain with 2-D interpolation (may have bug?)
 					 //
 					 heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-					 antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+					 antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 					 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 */
 					 if ( settings1->ALL_ANT_V_ON==0 ) {
 					   if (settings1->ANTENNA_MODE == 0){
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					   }
 					   if (settings1->ANTENNA_MODE == 1){
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type,k), 
+												    antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type,k),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					   }
 					 }
 					 else if ( settings1->ALL_ANT_V_ON==1 ) {
 					   if (settings1->ANTENNA_MODE == 0){
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, 0), 
+												    antenna_theta, antenna_phi, 0),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 }
 					   if (settings1->ANTENNA_MODE == 1){
 					   heff_lastbin = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-												    antenna_theta, antenna_phi, 0, k), 
+												    antenna_theta, antenna_phi, 0, k),
 								       freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					 }
 					 }
-					 
-					 
-					 
-					 
+
+
+
+
 					 // apply calpulser waveform
 					 // apply pol factor, heff
 					 if (event->IsCalpulser == 1){
@@ -1485,51 +1497,51 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   //cout<<"set signal pol as Vpol + Hpol for Calpulser2 evts"<<endl;
 					   Pol_vector = n_trg_slappy + n_trg_pokey;
 					 }
-					 
-					 
+
+
 					 //
 					 //
 					 for (int n=0; n<stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]/2; n++) {
-					   
-					   
+
+
 					   freq_tmp = dF_Nnew*((double)n+0.5);// in Hz 0.5 to place the middle of the bin and avoid zero freq
-					   
-					   
-					   
-					   
-					   
+
+
+
+
+
 					   //
 					   // apply ant factors (transmitter ant)
 					   //
 					   if ( settings1->ALL_ANT_V_ON==0 ) {
 					     if (settings1->ANTENNA_MODE == 0){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+											      ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					     }
 					   }
 					   else if ( settings1->ALL_ANT_V_ON==1 ) {
 					     if (settings1->ANTENNA_MODE == 0){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, 0), 
+											      ant_theta_trans, antenna_phi, 0),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					     }
 					     if (settings1->ANTENNA_MODE == 1){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      ant_theta_trans, antenna_phi, 0, k), 
+											      ant_theta_trans, antenna_phi, 0, k),
 								 freq_tmp, icemodel->GetN(event->Nu_Interaction[0].posnu) );
 					     }
 					   }
 					   //
 					   if ( n > 0 ) {
-					     
+
 					     if ( settings1->ALL_ANT_V_ON==0 ) {
-					       
+
 					       ApplyAntFactors_Tdomain_Transmitter( detector->GetAntPhase_1D( freq_tmp*1.e-6, ant_theta_trans, antenna_phi, detector->stations[i].strings[j].antennas[k].type ),
 										    heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
@@ -1537,56 +1549,56 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					       ApplyAntFactors_Tdomain_Transmitter( detector->GetAntPhase_1D( freq_tmp*1.e-6, ant_theta_trans, antenna_phi, 0 ),
 										    heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
-					     
-					     
-					     
+
+
+
 					   }
 					   else {
 					     ApplyAntFactors_Tdomain_FirstTwo( heff, heff_lastbin_trans, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
+
 					   //
 					   // apply ant factors (receiver ant)
 					   //
 					   /*
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-					     antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+					     antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 					     freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					   */
 					   if ( settings1->ALL_ANT_V_ON==0 ) {
 					     if (settings1->ANTENNA_MODE==0){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type), 
+											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type),
 								 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					     if (settings1->ANTENNA_MODE==1){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k), 
+											      antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type, k),
 								 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					   }
 					   else if ( settings1->ALL_ANT_V_ON==1 ) {
 					     if (settings1->ANTENNA_MODE ==0){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      antenna_theta, antenna_phi, 0), 
+											      antenna_theta, antenna_phi, 0),
 								 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					     if (settings1->ANTENNA_MODE ==1){
 					     heff = GaintoHeight(detector->GetGain_1D_OutZero(freq_tmp*1.E-6, // to MHz
-											      antenna_theta, antenna_phi, 0,k), 
+											      antenna_theta, antenna_phi, 0,k),
 								 freq_tmp, icemodel->GetN(detector->stations[i].strings[j].antennas[k]) );
 					     }
 					   }
-					   
 
-					   
+
+
 					   stations[i].strings[j].antennas[k].Heff[ray_sol_cnt].push_back( heff );
-					   
-					   
+
+
 					   if ( n > 0 ) {
-					     
+
 					     if ( settings1->ALL_ANT_V_ON==0 ) {
-					       
+
 					       ApplyAntFactors_Tdomain( detector->GetAntPhase_1D( freq_tmp*1.e-6, antenna_theta, antenna_phi, detector->stations[i].strings[j].antennas[k].type ),
 									heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
@@ -1594,14 +1606,14 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					       ApplyAntFactors_Tdomain( detector->GetAntPhase_1D( freq_tmp*1.e-6, antenna_theta, antenna_phi, 0 ),
 									heff, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1], settings1 );
 					     }
-					     
-					     
-					     
+
+
+
 					   }
 					   else {
 					     ApplyAntFactors_Tdomain_FirstTwo( heff, heff_lastbin, n_trg_pokey, n_trg_slappy, Pol_vector, detector->stations[i].strings[j].antennas[k].type, Pol_factor, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
+
 					   //
 					   // apply entire elect chain gain, phase
 					   //
@@ -1611,33 +1623,33 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   else {
 					     ApplyElect_Tdomain_FirstTwo( freq_tmp*1.e-6, freq_lastbin*1.e-6, detector, V_forfft[2*n], V_forfft[2*n+1] );
 					   }
-					   
-					   
-					   
+
+
+
 					 }// end for freq bin
-					 
-					 
+
+
 					 // now get time domain waveform back by inv fft
 					 Tools::realft(V_forfft,-1,stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt]);
-					 
-					 
+
+
 					 // we need to do normal time ordering as we did zero padding(?)
 					 // If signal is located at the center, we don't need to do NormalTimeOrdering???
 					 //Tools::NormalTimeOrdering(stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt], V_forfft);
-					 
-					 
+
+
 					 // skip linear interpolation for now
 					 Tools::SimpleLinearInterpolation_OutZero( stations[i].strings[j].antennas[k].Nnew[ray_sol_cnt], T_forfft, V_forfft, settings1->NFOUR/2, T_forint, volts_forint );
-					 
+
 					 // check what we save as V[], volts_forint? or volts_forfft
-					 
-					 
-					 
-					 
-					 
-					 
+
+
+
+
+
+
 					 for (int n=0; n<settings1->NFOUR/2; n++) {
-					   
+
 					   if (settings1->TRIG_ANALYSIS_MODE != 2) { // not pure noise mode (we need signal)
 					     //stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( volts_forfft[n] );
 					     //stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( V_forfft[n] * 2./(double)(settings1->NFOUR/2) ); // 2/N for inverse FFT normalization factor
@@ -1647,9 +1659,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 					   else if (settings1->TRIG_ANALYSIS_MODE == 2) { // pure noise mode (set signal to 0)
 					     stations[i].strings[j].antennas[k].V[ray_sol_cnt].push_back( 0. );
 					   }
-					   
+
 					 }
-					 
+
                                        }// Calpulser events
 
                                    } // if SIMULATION_MODE = 1
@@ -1682,17 +1694,17 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                                    ray_sol_cnt++;
-                               
+
 
                                }// end while number of solutions
-                           
+
                            }// end if solution exist
 
                            else {
-                               
+
                                //cout<<"station["<<i<<"].strings["<<j<<"].antennas["<<k<<"].trg = "<<stations[i].strings[j].antennas[k].trg[ray_sol_cnt]<<"  No vmmhz1m data!"<<endl;
                            }
-                       
+
 
                        }// end if posnu selected
 
@@ -1704,9 +1716,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 
                        stations[i].strings[j].antennas[k].ray_sol_cnt = ray_sol_cnt;    // save number of RaySolver solutions
-           
+
                        stations[i].Total_ray_sol += ray_sol_cnt; // add ray_sol_cnt to Total_ray_sol
-                       
+
 
                    }// for number_of_antennas_string
 
@@ -1764,7 +1776,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
            if (stations[i].Total_ray_sol) { // if there is any ray_sol (don't check trigger if there is no ray_sol at all)
            //if (stations[i].Total_ray_sol && settings1->TRIG_ANALYSIS_MODE != 2) { // if there is any ray_sol (don't check trigger if there is no ray_sol at all) and TRIG_ANALYSIS_MODE is 0 (signal + noise mode)
 
-                                   
+
 
                //cout<<"3"<<endl;
 
@@ -1818,8 +1830,8 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 //                   if ( settings1->NOISE==1 && settings1->DETECTOR==4) {
 //                       detector->ReadRayleigh_Station(settings1);
 //                   }
-                   
-                   
+
+
                    // reset Trigger class noise temp values
                    trigger->Reset_V_noise_freqbin(settings1, detector);
 
@@ -1834,7 +1846,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                if ( debugmode == 1 ) N_noise = 1;
                // now, check if DATA_BIN_SIZE is enough for total time delay between antennas
                else {
-               
+
                    N_noise = (int)( max_total_bin / settings1->DATA_BIN_SIZE ) + 1;
                }
                //cout<<"N_noise : "<<N_noise<<endl;
@@ -1904,7 +1916,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 			   //                           cout<<"noise_ID for "<<l<<"th noisewaveform is : "<<noise_ID[l]<<"  N_noise : "<<N_noise<<" ray_sol_cnt : "<<stations[i].strings[j].antennas[k].ray_sol_cnt<<endl;
 
-                       
+
 
                            // do only if it's not in debugmode
                            if ( debugmode == 0 ) {
@@ -2002,7 +2014,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                            } // if we are not in debug mode
 
 
-			
+
                        }
 
                        // currently there is a initial spoiled bins (maxt_diode_bin) at the initial Full_window "AND" at the initial of connected noisewaveform (we can fix this by adding values but not accomplished yet)
@@ -2072,7 +2084,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                            for (int m=0; m<stations[i].strings[j].antennas[k].ray_sol_cnt; m++) {   // loop over raysol numbers
                                // when ray_sol_cnt == 0, this loop inside codes will not run
 
-                               
+
                                if ( m==0 ) {    // if it's first sol
 
                                    if ( connect_signals[m] == 1 ) {
@@ -2161,9 +2173,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                            //
                            if ( settings1-> USE_MANUAL_GAINOFFSET == 1 )
                                Apply_Gain_Offset(settings1, trigger, detector, ch_ID, i ); // last i for stationID
-                       
-                       
-                       
+
+
+
                        } // if it's not debugmode
 
 
@@ -2175,7 +2187,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                } // for strings
 
 
-                       
+
 
                // do only if it's not in debugmode
                if ( debugmode == 0 ) {
@@ -2187,7 +2199,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                //
 
 
-               
+
                int trig_i, trig_j, trig_bin;
                int trig_search_init;
 
@@ -2205,9 +2217,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                // global trigger mode
                // 0 for orginal N_TRIG out of 16 channels
                // 1 for new stations, N_TRIG_V out of Vpol channels or N_TRIG_H out of Hpol channels
-               
+
                int check_ch;
-               
+
                //trig_i = trigger->maxt_diode_bin;
                //trig_i = trigger->maxt_diode_bin + settings1->NFOUR; // give some time shift for mimicing force trig events
                trig_search_init = trigger->maxt_diode_bin + settings1->NFOUR; // give some time shift for mimicing force trig events
@@ -2220,31 +2232,104 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
 	       if(settings1->TRIG_SCAN_MODE==0){// ******************** old mode left as-is ********************
 
-               // avoid really long trig_window_bin case (change trig_window to check upto max_total_bin)
-               if (max_total_bin - trig_window_bin <= trig_i) trig_window_bin = max_total_bin - trig_i -1;
-	       
-	       
-               //while (trig_i < settings1->DATA_BIN_SIZE - trig_window_bin ) {
-               while (trig_i < max_total_bin - trig_window_bin ) {
+                /*
+                    We need to add some logic to deal with what happens when we are running in A2 and A3 mode
+                    with config specific trigger delay settings
+                */
 
-                   N_pass = 0;
-                   N_pass_V = 0;
-                   N_pass_H = 0;
-                   last_trig_bin = 0;
-                   Passed_chs.clear();
+                // these must always be set
+                for(int localchan=0; localchan<16; localchan++){
+                    triggerDelay[localchan]=0;
+                    mostDelay=0;
+                }
 
+                if(settings1->DETECTOR==4 && settings1->DETECTOR_STATION_LIVETIME_CONFIG>0){ // if emulating a real station, and we want config selection power
 
-                   //for ( trig_j=0; trig_j<ch_ID; trig_j++) {    // loop over all channels
-                   trig_j = 0;
-                   while (trig_j < ch_ID ) {
+                    if(settings1->DETECTOR_STATION==2){ // if station 2
 
-                       int string_i = detector->getStringfromArbAntID( i, trig_j);
-                       int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
+                        if(settings1->DETECTOR_STATION_LIVETIME_CONFIG==2 || settings1->DETECTOR_STATION_LIVETIME_CONFIG==5){ // if config 5 or 5 in A2
+                            triggerDelay[4] = 81.4 + 100;
+                            triggerDelay[5] = 73.2 + 100;
+                            triggerDelay[6] = 15.4 + 100;
+                            triggerDelay[7] = 7.2  + 100;
 
-                       int channel_num = detector->GetChannelfromStringAntenna ( i, string_i, antenna_i, settings1 );
-                       // check if we want to use BH chs only for trigger analysis
-                       //if (settings1->TRIG_ONLY_BH_ON == 1) {
-                       if ( (settings1->TRIG_ONLY_BH_ON == 1)&&(settings1->DETECTOR==3) ) { // trig by BH is only for TestBed case
+                            // string 0 = D2, string 2 = D4, string3 = D1
+                            triggerDelay[0] = triggerDelay[8] = triggerDelay[12]  = 81.4;
+                            triggerDelay[1] = triggerDelay[9] = triggerDelay[13]  = 73.2;
+                            triggerDelay[2] = triggerDelay[10] = triggerDelay[14] = 15.4;
+                            triggerDelay[3] = triggerDelay[11] = triggerDelay[15] = 7.2;
+
+                            mostDelay = triggerDelay[4];
+
+                        }
+                    }
+
+                    if(settings1->DETECTOR_STATION==3){
+
+                        if(settings1->DETECTOR_STATION_LIVETIME_CONFIG==2 || settings1->DETECTOR_STATION_LIVETIME_CONFIG==4){ // if config 2 or 4 in A3
+
+                            // string 0 = D2, order 0-3 BV-BH-TV-TH
+                            triggerDelay[0] = 81.4 + 100;
+                            triggerDelay[1] = 73.2 + 100;
+                            triggerDelay[2] = 15.4 + 100;
+                            triggerDelay[3] = 7.2  + 100;
+
+                            // string 1 = D3, string 2 = D4, string3 = D1
+                            triggerDelay[4] = triggerDelay[8] = triggerDelay[12]  = 81.4;
+                            triggerDelay[5] = triggerDelay[9] = triggerDelay[13]  = 73.2;
+                            triggerDelay[6] = triggerDelay[10] = triggerDelay[14] = 15.4;
+                            triggerDelay[7] = triggerDelay[11] = triggerDelay[15] = 7.2;
+
+                            mostDelay = triggerDelay[0];
+
+                        }
+                    }
+                }
+
+               // avoid really long trig_window_bin case (change trig_window to check upto max_total_bin)
+               if (max_total_bin - trig_window_bin <= trig_i) trig_window_bin = max_total_bin - trig_i -1;
+
+
+               //while (trig_i < settings1->DATA_BIN_SIZE - trig_window_bin ) {
+               while (trig_i < max_total_bin - trig_window_bin ) {
+
+                   N_pass = 0;
+                   N_pass_V = 0;
+                   N_pass_H = 0;
+                   last_trig_bin = 0;
+                   Passed_chs.clear();
+
+
+                   //for ( trig_j=0; trig_j<ch_ID; trig_j++) {    // loop over all channels
+                   trig_j = 0;
+                   while (trig_j < ch_ID ) {
+
+
+                    // need to mask out a trigger channel when necessary
+                    // which is when emulating real station 2 in config 3-5 only
+                    if(settings1->DETECTOR==4 && settings1->DETECTOR_STATION==2){
+                        if(settings1->DETECTOR_STATION_LIVETIME_CONFIG>2){
+                            if(trig_j==9){
+                                trig_j++;
+                                continue;
+                            }
+                        }
+                    }
+
+                       int offset=0;
+                       if(settings1->DETECTOR==4){
+                           // only try to calculate the offset of DETECTOR=4, and we can guarantee that there will be an entry for triggerDelay[trig_j]
+                           // otherwise, if someone simulates an ideal station and changes the number of channels, this will segfault in a very hard to debug way
+                           offset = int((mostDelay -  triggerDelay[trig_j]) / (settings1->TIMESTEP * 1e9));
+                       }
+
+                       int string_i = detector->getStringfromArbAntID( i, trig_j);
+                       int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
+
+                       int channel_num = detector->GetChannelfromStringAntenna ( i, string_i, antenna_i, settings1 );
+                       // check if we want to use BH chs only for trigger analysis
+                       //if (settings1->TRIG_ONLY_BH_ON == 1) {
+                       if ( (settings1->TRIG_ONLY_BH_ON == 1)&&(settings1->DETECTOR==3) ) { // trig by BH is only for TestBed case
 
                            // check if this channel is BH ch (DAQchan)
                            if ( detector->stations[i].strings[string_i].antennas[antenna_i].DAQchan == 0 ) {
@@ -2256,7 +2341,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                    if ( settings1->NOISE_CHANNEL_MODE==0) {
                                        // with threshold offset by chs
-				     if ( trigger->Full_window[trig_j][trig_i+trig_bin] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
+				                        if ( trigger->Full_window[trig_j][trig_i+trig_bin] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
                                            //cout<<"trigger passed at bin "<<trig_i+trig_bin<<" ch : "<<trig_j<<endl;
                                            //stations[i].strings[(int)((trig_j)/4)].antennas[(int)((trig_j)%4)].Trig_Pass = trig_i+trig_bin;
                                            stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i+trig_bin;
@@ -2317,7 +2402,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                            }
 
                        }
-                       
+
 
 
 
@@ -2427,10 +2512,11 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                if ( settings1->NOISE_CHANNEL_MODE==0) {
                                    // with threshold offset by chs
-                                   if ( trigger->Full_window[trig_j][trig_i+trig_bin] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
+                                   if( trig_i+offset+trig_bin >= settings1->DATA_BIN_SIZE ) break; //if trigger window hits wf end, cannot scan this channel further with this trig_i
+                                   if ( trigger->Full_window[trig_j][trig_i+trig_bin+offset] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
                                        //cout<<"trigger passed at bin "<<trig_i+trig_bin<<" ch : "<<trig_j<<endl;
                                        //stations[i].strings[(int)((trig_j)/4)].antennas[(int)((trig_j)%4)].Trig_Pass = trig_i+trig_bin;
-                                       stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i+trig_bin;
+                                       stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i+trig_bin+offset;
                                        N_pass++;
                                        if (detector->stations[i].strings[string_i].antennas[antenna_i].type == 0) { // Vpol
                                            N_pass_V++;
@@ -2445,8 +2531,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                }
                                else if ( settings1->NOISE_CHANNEL_MODE==1) {
                                    // with threshold offset by chs
-                                   if ( trigger->Full_window[trig_j][trig_i+trig_bin] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
-                                       stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i+trig_bin;
+                                   if( trig_i+offset+trig_bin >= settings1->DATA_BIN_SIZE ) break; //if trigger window hits wf end, cannot scan this channel further with this trig_i
+                                   if ( trigger->Full_window[trig_j][trig_i+trig_bin+offset] < (detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1) ) ) {   // if this channel passed the trigger!
+                                       stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i+trig_bin+offset;
                                        N_pass++;
                                        if (detector->stations[i].strings[string_i].antennas[antenna_i].type == 0) { // Vpol
                                            N_pass_V++;
@@ -2545,7 +2632,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                    if ( stations[i].strings[string_i].antennas[antenna_i].SignalExt[m] ) {
 
                                        dBin = abs( stations[i].strings[string_i].antennas[antenna_i].SignalBin[m] - stations[i].strings[string_i].antennas[antenna_i].Trig_Pass );
-               
+
                                        if ( dBin < mindBin ) {
                                            stations[i].strings[string_i].antennas[antenna_i].Likely_Sol = m; // store the ray sol number which is minimum difference between Trig_Pass bin
                                            mindBin = dBin;
@@ -2556,7 +2643,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                                }
 
 
-                               
+
                                //skip this passed ch as it already has bin info
                                //cout<<"trigger passed at bin "<<stations[i].strings[(int)((ch_loop)/4)].antennas[(int)((ch_loop)%4)].Trig_Pass<<"  passed ch : "<<ch_loop<<" Direct dist btw posnu : "<<event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[(int)((ch_loop)/4)].antennas[(int)((ch_loop)%4)] )<<endl;
                                //cout<<endl<<"trigger passed at bin "<<stations[i].strings[string_i].antennas[antenna_i].Trig_Pass<<"  passed ch : "<<ch_loop<<" ("<<detector->stations[i].strings[string_i].antennas[antenna_i].type<<"type) Direct dist btw posnu : "<<event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[string_i].antennas[antenna_i] )<<" noiseID : "<<stations[i].strings[string_i].antennas[antenna_i].noise_ID[0];
@@ -2589,7 +2676,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                                // now save the voltage waveform to V_mimic
                                //
-                               
+
                                for (int mimicbin=0; mimicbin < waveformLength; mimicbin++) {
 
                                    // new DAQ waveform writing mechanism test
@@ -2625,7 +2712,7 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 
                            }
                            else {
-                               //stations[i].strings[(int)((ch_loop)/4)].antennas[(int)((ch_loop)%4)].Trig_Pass = stations[i].Global_Pass + settings1->NFOUR/4;   // so that global trig is 
+                               //stations[i].strings[(int)((ch_loop)/4)].antennas[(int)((ch_loop)%4)].Trig_Pass = stations[i].Global_Pass + settings1->NFOUR/4;   // so that global trig is
                                //stations[i].strings[(int)((ch_loop)/4)].antennas[(int)((ch_loop)%4)].Trig_Pass = 0.;
                                stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = 0.;
 
@@ -2731,18 +2818,18 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
                }    // while trig_i
 
 	       }// if TRIG_SCAN_MODE==0
-	       
+
 	       else if(settings1->TRIG_SCAN_MODE>0) triggerCheckLoop(settings1, detector, event, trigger, i, trig_search_init, max_total_bin, trig_window_bin, settings1->TRIG_SCAN_MODE);
-	       
+
 // 	       else if(settings1->TRIG_SCAN_MODE==2) triggerCheckLoopScan();
-	       
+
 // 	       else if(settings1->TRIG_SCAN_MODE==3) triggerCheckLoopScanNumbers();
-                       
+
            } // if it's not debugmode
 
 
 
-                   // delete noise waveforms 
+                   // delete noise waveforms
        if (settings1->NOISE_WAVEFORM_GENERATE_MODE == 0) {// noise waveforms will be generated for each evts
            // remove noise waveforms for next evt
            trigger->ClearNoiseWaveforms();
@@ -2774,9 +2861,9 @@ void Report::Connect_Interaction_Detector (Event *event, Detector *detector, Ray
 }   // end Connect_Interaction_Detector
 
 int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int scan_mode ){
- 
+
   class CircularBuffer {
-    
+
   public:
     int i;
     int mode; // in mode 1 only check number of values above threshold, in >1 check what the best value is too
@@ -2789,59 +2876,59 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
     double epsilon; // best value needs to be this close to current last value
     double last_value; // value leaving buffer
     int addToNPass; // number of values above pthresh inside buffer
-    
-    
-    
+
+
+
     CircularBuffer(int size, double threshold, int scan_mode) : N(size), pthresh(threshold), mode(scan_mode) {i=0; best_value=0; temp_value=0; last_value=0; addToNPass=0; epsilon=1e-6; buffer=new double[N]; for(int j=0;j<N;j++) buffer[j]=0;}
-    
+
     ~CircularBuffer(){ delete [] buffer; }
-    
+
     int add(double input_value){
 
       changelog=0;
       temp_value=best_value;
-      
+
       if(buffer[i]<pthresh) addToNPass--; // if the value leaving the buffer is over threshold, we reduce the counter.
       if(mode>1) last_value=buffer[i];// in mode 1 we don't care about the values, just about the addToNPass
-	      
+
       if(input_value<pthresh){
-	
+
 	addToNPass++; // if value entering buffer is over threshold we increase the counter.
         buffer[i]=input_value;
-	
+
       }
       else buffer[i]=0; // if under threshold just insert zero
-      
+
       if(mode>1&&buffer[i]<best_value){ best_value=buffer[i]; temp_value=best_value; changelog=1;}// improve best threshold value in the buffer
 
       if(mode>1&&std::fabs(last_value-best_value)<epsilon){ // i.e. if last_value==best_value. this happens when the best value leaves buffer
-      
+
 	best_value=findBestValue(); // rescan whole buffer. this should be rather rare...
 	temp_value=best_value;
 	changelog=1;
       }
-      
-           
+
+
       i++;
       if(i==N) i=0;
-            
+
       return changelog; // in mode>1: return value is zero if no changes, and non-zero if there are changes to best_value (for mode==1 it's always zero);
-      
-    }// add 
+
+    }// add
     int fill(double input_value){// buffer is just filling, don't use last_value
-      
+
       changelog=0;
       temp_value=best_value;
-      
+
       if(input_value<pthresh){
-	
+
 	addToNPass++; // if value entering buffer is over threshold we increase the counter.
         buffer[i]=input_value;
 // 	cout<<"addToNPass++\n";
-	
+
       }
       else buffer[i]=0; // if under threshold add just zero
-      
+
       if(mode>1&&buffer[i]<best_value){ best_value=buffer[i]; temp_value=best_value; changelog=1;}// improve best threshold value in the buffer
 
       i++;
@@ -2850,28 +2937,28 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
       return changelog;
 
     }// fill
-    
+
     double findBestValue(){
-      
+
       double temp_best=0;
-      
+
       for(int ii=0;ii<N;ii++) if(buffer[ii]<temp_best) {
-	
+
 	temp_best=buffer[ii];
-	
+
       }
-     
+
       return temp_best;
-      
+
     }// find best value
-    
+
     int numBinsToOldestTrigger(){
-     
+
       if(addToNPass<1){ cerr<<"ERROR: there are no triggers in this buffer right now!\n"; return -1;}
-      int j; // the number of bins after "i" where the first trigger is found 
-      
+      int j; // the number of bins after "i" where the first trigger is found
+
       for(j=1; j<N; j++){
-	
+
 // 	if(i==0&&buffer[N-1]<0) return 1;
 	// i-1 is b/c we did i++ in the last call to add/fill.
 	if(buffer[(i-1+j)%N]<0) break;// if there's any value here, its because it passed the threshold, so take it
@@ -2879,87 +2966,87 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
       }// for j
 
 //       if(j==0) return 0;
-      return N-j; // the backward count of how many bins between i and the earliest trigger... 
-      
+      return N-j; // the backward count of how many bins between i and the earliest trigger...
+
     }// numBinsToOldestTrigger
-    
+
     int numBinsToLatestTrigger(){
-     
+
       if(addToNPass<1){ cerr<<"ERROR: there are no triggers in this buffer right now!\n"; return -1;}
-      int j; // the number of bins after "i" where the first trigger is found 
-      
+      int j; // the number of bins after "i" where the first trigger is found
+
       for(j=0; j<N; j++){
-	
+
 	int bin=i-1-j;
 	if(bin<0) bin=N+(i-j);
-	
+
 	if(buffer[bin]<0){// if there's any value here, its because it passed the threshold, so take it
 
 	    break;
 
 	}
-	
+
       }// for j
-      
-      return j; // the count of how many bins between i and the latest trigger... 
-      
+
+      return j; // the count of how many bins between i and the latest trigger...
+
     }// numBinsToLatestTrigger
-    
+
   };
   int i=stationID;
-  
+
   int numChan=stations[i].TDR_all.size();
   int numChanVpol=stations[i].TDR_Vpol_sorted.size();
   int numChanHpol=stations[i].TDR_Hpol_sorted.size();
-  
+
 
   double powerthreshold=settings1->POWERTHRESHOLD;
-  // this value is compared to POWERTHRESHOLD for local trigger.  
-  
+  // this value is compared to POWERTHRESHOLD for local trigger.
+
   int first_trigger=0;
-  
+
   double Pthresh_value[numChan];
   CircularBuffer **buffer=new CircularBuffer*[numChan];
   for(int trig_j=0;trig_j<numChan; trig_j++){// initialize Trig_Pass and buffers
-    
+
     Pthresh_value[trig_j]=0;
     buffer[trig_j]=new CircularBuffer( trig_window_bin, powerthreshold, scan_mode);
-        
+
     int string_i = detector->getStringfromArbAntID( i, trig_j);
     int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
-    
+
     stations[i].strings[string_i].antennas[antenna_i].SingleChannelTriggers=0;
     stations[i].strings[string_i].antennas[antenna_i].TotalBinsScannedPerChannel=0;
-    
+
 //     int string_i = detector->getStringfromArbAntID( i, trig_j);
 //     int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
 //     stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = 0.;
-    
+
   }// for trig_j
-  
+
   double *TDR_all_sorted_temp;
   double *TDR_Vpol_sorted_temp;
   double *TDR_Hpol_sorted_temp;
-  
+
   if(scan_mode>1){
-    
+
     TDR_all_sorted_temp=new double[numChan];
     TDR_Vpol_sorted_temp=new double[numChanVpol];
     TDR_Hpol_sorted_temp=new double[numChanHpol];
-    
+
     // only need to initialize for scan_mode>1
     for(int trig_j=0;trig_j<numChan;trig_j++) TDR_all_sorted_temp[trig_j]=0;
     for(int trig_j=0;trig_j<numChanVpol;trig_j++) TDR_Vpol_sorted_temp[trig_j]=0;
     for(int trig_j=0;trig_j<numChanHpol;trig_j++) TDR_Hpol_sorted_temp[trig_j]=0;
-          
+
   }// if scan_mode>1
 
   int global_pass_bit=0;
   int check_TDR_configuration=0; // check if we need to reorder our TDR arrays
-  int SCTR_cluster_bit[numChan];   
-  
+  int SCTR_cluster_bit[numChan];
+
   for(int trig_j=0;trig_j<numChan;trig_j++) SCTR_cluster_bit[trig_j]=0;
-  
+
   for(int trig_i = trig_search_init; trig_i < max_total_bin; trig_i++) { // scan the different window positions
 
     // for trigger check:
@@ -2968,160 +3055,160 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
     int N_pass_H = 0;
 
     check_TDR_configuration=0;
-      
+
     for (int trig_j=0; trig_j<numChan; trig_j++){
-      
+
       int string_i = detector->getStringfromArbAntID( i, trig_j);
       int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
-      
+
       if (settings1->TRIG_ONLY_BH_ON==0
-	               || 
+	               ||
          (settings1->TRIG_ONLY_BH_ON==1 && settings1->DETECTOR==3 && detector->stations[i].strings[string_i].antennas[antenna_i].DAQchan==0)
                        ||
 	 (settings1->TRIG_ONLY_LOW_CH_ON==1 && settings1->DETECTOR!=3 && antenna_i<2 ) ){ // channel filter: choose if to use lower/borehole channels or not
-      
+
 
       int channel_num = detector->GetChannelfromStringAntenna ( i, string_i, antenna_i, settings1 );
 
-      // assign Pthresh a value 
+      // assign Pthresh a value
       if(settings1->NOISE_CHANNEL_MODE==0) Pthresh_value[trig_j]=trigger->Full_window[trig_j][trig_i]/(trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1) );
       if(settings1->NOISE_CHANNEL_MODE==1) Pthresh_value[trig_j]=trigger->Full_window[trig_j][trig_i]/(trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1) );
       if(settings1->NOISE_CHANNEL_MODE==2){
-	  
+
 	  if(channel_num-1 < 8) Pthresh_value[trig_j]=trigger->Full_window[trig_j][trig_i]/(trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1) );
 	  else Pthresh_value[trig_j]=trigger->Full_window[trig_j][trig_i]/(trigger->rmsdiode_ch[8] * detector->GetThresOffset( i, channel_num-1,settings1) );
-	  
+
 	}
-	// this is to count how many local trigger clusters there are 
+	// this is to count how many local trigger clusters there are
       if(Pthresh_value[trig_j]<powerthreshold){
-	
+
 	if(SCTR_cluster_bit[trig_j]==0) stations[i].strings[string_i].antennas[antenna_i].SingleChannelTriggers++;
-		
+
 	// records all the different Pthresh values that caused local trigger.
-        if(settings1->TRIG_SCAN_MODE>2){ 
-	  
+        if(settings1->TRIG_SCAN_MODE>2){
+
 	  if(SCTR_cluster_bit[trig_j]==0){// if first trigger in cluster
-	    
+
 	    stations[i].strings[string_i].antennas[antenna_i].SCT_threshold_pass.push_back(Pthresh_value[trig_j]);
-	    
-	    
+
+
 	  }
 	  else{// choose the highest trigger value (most negative) in cluster
-	   
+
 	    if(Pthresh_value[trig_j]<stations[i].strings[string_i].antennas[antenna_i].SCT_threshold_pass.back()) stations[i].strings[string_i].antennas[antenna_i].SCT_threshold_pass.back()=Pthresh_value[trig_j];
-	    
+
 	  }
-	  
+
 	}// trig scan mode > 2
-	
+
 	SCTR_cluster_bit[trig_j]=1;
-	
+
       }// if local trigger
       else SCTR_cluster_bit[trig_j]=0;// if no local trigger, set zero to start a new cluster at next local trigger
-      
+
       // and how many bins scanned
       stations[i].strings[string_i].antennas[antenna_i].TotalBinsScannedPerChannel++;
-      
 
 
-      
-      						    
+
+
+
       // fill the buffers (if any changes occur mark check_TDR_configuration as non-zero)
       if(trig_i<trig_search_init+trig_window_bin) check_TDR_configuration+=buffer[trig_j]->fill(Pthresh_value[trig_j]);
       else check_TDR_configuration+=buffer[trig_j]->add(Pthresh_value[trig_j]);
-	
+
       if(buffer[trig_j]->addToNPass>0){// if there is at least one value above threshold in the buffer, this is ++
-	  
+
 	N_pass++;
 	if(detector->stations[i].strings[string_i].antennas[antenna_i].type == 0) N_pass_V++;
 	if(detector->stations[i].strings[string_i].antennas[antenna_i].type == 1) N_pass_H++;
 
-	  
-// 	  if(last_trig_bin<trig_i) last_trig_bin=trig_i;// not sure we need this variable in this mode... 
-	  
+
+// 	  if(last_trig_bin<trig_i) last_trig_bin=trig_i;// not sure we need this variable in this mode...
+
        }// if addToNPass>0
-	
+
       }// non-testbed case (i.e. use all channels)
-      
+
     }// for trig_j (channel scan)
 
     // check if global trigger...
-    
-    if( (settings1->TRIG_MODE==0&&( N_pass >= settings1->N_TRIG )) || 
-	(settings1->TRIG_MODE==1&&( N_pass_V >= settings1->N_TRIG_V || 
+
+    if( (settings1->TRIG_MODE==0&&( N_pass >= settings1->N_TRIG )) ||
+	(settings1->TRIG_MODE==1&&( N_pass_V >= settings1->N_TRIG_V ||
 				    N_pass_H >= settings1->N_TRIG_H )
-	 ) 
+	 )
 	//|| (settings1->TRIG_MODE==2&&( N_pass_0 >= settings1->N_TRIG_0 || N_pass_1 >= settings1->N_TRIG_1 ))
 	){ // if there's a trigger !
-      
 
-      global_pass_bit=1;  
+
+      global_pass_bit=1;
       if(first_trigger==0){ // if this is the first trigger, mark this position and save event
 
 	first_trigger=1;
 
 	for(int trig_j=0;trig_j<numChan;trig_j++){
-	 
+
 	  int string_i = detector->getStringfromArbAntID( i, trig_j);
 	  int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
 // 	  if(buffer[trig_j]->addToNPass>0) stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i-buffer[trig_j]->numBinsToLatestTrigger(); // mark the bin on which we triggered...
 	  if(buffer[trig_j]->addToNPass>0) stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = trig_i-buffer[trig_j]->numBinsToOldestTrigger(); // mark the bin on which we triggered...
 	  else stations[i].strings[string_i].antennas[antenna_i].Trig_Pass = 0.;
-	  
+
 	}// for trig_j
-	
+
 	saveTriggeredEvent(settings1, detector, event, trigger, stationID, trig_search_init, max_total_bin, trig_window_bin, trig_i);
 // 	cout<<"\nPthresh value=";
 // 	if(scan_mode==1) for(int trig_j=0;trig_j<numChan; trig_j++) cout<<" "<<Pthresh_value[trig_j];
 // 	if(scan_mode>1)  for(int trig_j=0;trig_j<numChan; trig_j++) cout<<" "<<buffer[trig_j]->best_value;
 // 	cout<<"\n";
-	
+
       }// first trigger
-      
+
 //       if(scan_mode==1) return last_trig_bin; //  if we aren't going to scan all the Pthresh values, just return
       if(scan_mode==1) return trig_i; //  if we aren't going to scan all the Pthresh values, just return
     }
     else global_pass_bit=0;// no trigger
-    
+
     if(scan_mode>1&&check_TDR_configuration&&global_pass_bit){// if there's a trigger and anything changes in the buffers, restock the TDR arrays
-      	    
+
       for(int trig_j=0;trig_j<numChan;trig_j++) TDR_all_sorted_temp[trig_j]=0;
       for(int trig_j=0;trig_j<numChanVpol;trig_j++) TDR_Vpol_sorted_temp[trig_j]=0;
       for(int trig_j=0;trig_j<numChanHpol;trig_j++) TDR_Hpol_sorted_temp[trig_j]=0;
 
-      for(int trig_j=0;trig_j<numChan;trig_j++){// fill the TDR (unsorted) arrays if they improved... 
-	
+      for(int trig_j=0;trig_j<numChan;trig_j++){// fill the TDR (unsorted) arrays if they improved...
+
 	if(buffer[trig_j]->best_value<stations[i].TDR_all[trig_j]) stations[i].TDR_all[trig_j]=buffer[trig_j]->best_value;
 
       }// for trig_j
 
       if(settings1->TRIG_MODE==0){ // for N out of 16 mode
-      
+
 	if(N_pass>=settings1->N_TRIG) for(int ii=0;ii<N_pass; ii++){// find the N_pass best channel's TDR and store them.
-	 
+
 	  double best_thresh=0;
 	  int best_chan=0;
-	  
+
 	  for(int trig_j=0;trig_j<numChan;trig_j++) if(buffer[trig_j]->temp_value<best_thresh){ best_thresh=buffer[trig_j]->temp_value; best_chan=trig_j;}
-	  
+
 	  buffer[best_chan]->temp_value=0;
-	  
+
 	  TDR_all_sorted_temp[ii]=best_thresh;
-	  
+
 	}// for ii
-	
-	
+
+
 	// debug output:
 	if(TDR_all_sorted_temp[0]>TDR_all_sorted_temp[1]||TDR_all_sorted_temp[1]>TDR_all_sorted_temp[2]){
-	   
+
 	  cout<<"\n";
 	  for(int p=0;p<80;p++) cout<<"*";
 	  cout<<"\n  ordering problem: "<<TDR_all_sorted_temp[0]<<" "<<TDR_all_sorted_temp[1]<<" "<<TDR_all_sorted_temp[2]<<"\n";
 	  for(int p=0;p<80;p++) cout<<"*";
 	  cout<<"\n";
-	    
+
 	}
-	
+
       }// if trig_mode==0
       if(settings1->TRIG_MODE==1){ // for N out of either polarization
 
@@ -3130,75 +3217,75 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
 
 	  double best_thresh=0;
 	  int best_chan=0;
-	  
+
 	  for(int trig_j=0;trig_j<numChan;trig_j++){
-	    
+
 	    int string_i = detector->getStringfromArbAntID( i, trig_j);
-	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);	 
+	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
+
+	    if(detector->stations[i].strings[string_i].antennas[antenna_i].type == 0&&buffer[trig_j]->temp_value<best_thresh){
 
-	    if(detector->stations[i].strings[string_i].antennas[antenna_i].type == 0&&buffer[trig_j]->temp_value<best_thresh){ 
-	      
-	      best_thresh=buffer[trig_j]->temp_value; 
+	      best_thresh=buffer[trig_j]->temp_value;
 	      best_chan=trig_j;
-	      
+
 	    }// if best
 	  }// for trig_j
 	  buffer[best_chan]->temp_value=0;
-	  
+
 	  TDR_Vpol_sorted_temp[ii]=best_thresh;
-	  
+
 	}// for ii
-	  
+
 	  // debug output:
 // 	  if(TDR_Vpol_sorted_temp[0]>TDR_Vpol_sorted_temp[1]||TDR_Vpol_sorted_temp[1]>TDR_Vpol_sorted_temp[2]){
-// 	   
+//
 // 	    cout<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n  ordering problem, Vpol: "<<TDR_Vpol_sorted_temp[0]<<" "<<TDR_Vpol_sorted_temp[1]<<" "<<TDR_Vpol_sorted_temp[2]<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n";
-// 	    
+//
 // 	  }
 	// for Hpol only
 	if(N_pass_H>=settings1->N_TRIG_H) for(int ii=0;ii<N_pass_H; ii++){// find the N_pass best channel's TDR and store them.
 
 	  double best_thresh=0;
 	  int best_chan=0;
-	  
-	  for(int trig_j=0;trig_j<numChan;trig_j++){ 
-	    
+
+	  for(int trig_j=0;trig_j<numChan;trig_j++){
+
 	    int string_i = detector->getStringfromArbAntID( i, trig_j);
 	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
-	 
-	    if(detector->stations[i].strings[string_i].antennas[antenna_i].type==1&&buffer[trig_j]->temp_value<best_thresh){ 
-	      
-	      best_thresh=buffer[trig_j]->temp_value; 
+
+	    if(detector->stations[i].strings[string_i].antennas[antenna_i].type==1&&buffer[trig_j]->temp_value<best_thresh){
+
+	      best_thresh=buffer[trig_j]->temp_value;
 	      best_chan=trig_j;
-	      
+
 	    }// if best
 	  }// for trig_j
-	
+
 	  buffer[best_chan]->temp_value=0;
-	  
+
 	  TDR_Hpol_sorted_temp[ii]=best_thresh;
-	  
 
-	  	  
+
+
 	}// for ii
-	
+
 //           // debug output:
 // 	  if(TDR_Hpol_sorted_temp[0]>TDR_Hpol_sorted_temp[1]||TDR_Hpol_sorted_temp[1]>TDR_Hpol_sorted_temp[2]){
-// 	   
+//
 // 	    cout<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n  ordering problem, Hpol: "<<TDR_Hpol_sorted_temp[0]<<" "<<TDR_Hpol_sorted_temp[1]<<" "<<TDR_Hpol_sorted_temp[2]<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n";
-// 	    
+//
 // 	  }
       }// if trig_mode==1
 
-      /*          
+      /*
       if(settings1->TRIG_MODE==2){ // for N out of arbitrary sets of antennas
 
 	// for Set 0 only:
@@ -3206,167 +3293,167 @@ int Report::triggerCheckLoop(Settings *settings1, Detector *detector, Event *eve
 
 	  double best_thresh=0;
 	  int best_chan=0;
-	  
+
 	  for(int trig_j=0;trig_j<numChan;trig_j++){
-	    
+
 	    int string_i = detector->getStringfromArbAntID( i, trig_j);
-	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);	 
+	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
 
-	    if((antenna_i == 0 || antenna_i == 2 ) && buffer[trig_j]->temp_value<best_thresh){ 
-	      
-	      best_thresh=buffer[trig_j]->temp_value; 
+	    if((antenna_i == 0 || antenna_i == 2 ) && buffer[trig_j]->temp_value<best_thresh){
+
+	      best_thresh=buffer[trig_j]->temp_value;
 	      best_chan=trig_j;
-	      
+
 	    }// if best
 	  }// for trig_j
 	  buffer[best_chan]->temp_value=0;
-	  
+
 	  TDR_Vpol_sorted_temp[ii]=best_thresh;
-	  
+
 	}// for ii
-	  
+
 	  // debug output:
 // 	  if(TDR_Vpol_sorted_temp[0]>TDR_Vpol_sorted_temp[1]||TDR_Vpol_sorted_temp[1]>TDR_Vpol_sorted_temp[2]){
-// 	   
+//
 // 	    cout<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n  ordering problem, Vpol: "<<TDR_Vpol_sorted_temp[0]<<" "<<TDR_Vpol_sorted_temp[1]<<" "<<TDR_Vpol_sorted_temp[2]<<"\n";
 // 	    for(int p=0;p<80;p++) cout<<"*";
 // 	    cout<<"\n";
-// 	    
+//
 // 	  }
 	// for Hpol only
 	if(N_pass_1>=settings1->N_TRIG_1) for(int ii=0;ii<N_pass_1; ii++){// find the N_pass best channel's TDR and store them.
 
 	  double best_thresh=0;
 	  int best_chan=0;
-	  
-	  for(int trig_j=0;trig_j<numChan;trig_j++){ 
-	    
+
+	  for(int trig_j=0;trig_j<numChan;trig_j++){
+
 	    int string_i = detector->getStringfromArbAntID( i, trig_j);
 	    int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
-	 
-	    if((antenna_i==1 || antenna_i == 3) && buffer[trig_j]->temp_value<best_thresh){ 
-	      
-	      best_thresh=buffer[trig_j]->temp_value; 
+
+	    if((antenna_i==1 || antenna_i == 3) && buffer[trig_j]->temp_value<best_thresh){
+
+	      best_thresh=buffer[trig_j]->temp_value;
 	      best_chan=trig_j;
-	      
+
 	    }// if best
 	  }// for trig_j
-	
+
 	  buffer[best_chan]->temp_value=0;
-	  
+
 	  TDR_Hpol_sorted_temp[ii]=best_thresh;
-	  
 
-	  	  
+
+
 	}// for ii
 */
 
-    
+
     // check if temp TDR arrays improved, if so update TDR arrays:
     if(settings1->TRIG_MODE==0){
-      
+
       if(N_pass>=settings1->N_TRIG) for(int ii=0;ii<N_pass;ii++) if(TDR_all_sorted_temp[ii]<stations[i].TDR_all_sorted[ii]) stations[i].TDR_all_sorted[ii]=TDR_all_sorted_temp[ii];
-      
+
     }
     if(settings1->TRIG_MODE==1){
-     
+
       if(N_pass_V>=settings1->N_TRIG_V) for(int ii=0;ii<N_pass_V;ii++) if(TDR_Vpol_sorted_temp[ii]<stations[i].TDR_Vpol_sorted[ii]) stations[i].TDR_Vpol_sorted[ii]=TDR_Vpol_sorted_temp[ii];
       if(N_pass_H>=settings1->N_TRIG_H) for(int ii=0;ii<N_pass_H;ii++) if(TDR_Hpol_sorted_temp[ii]<stations[i].TDR_Hpol_sorted[ii]) stations[i].TDR_Hpol_sorted[ii]=TDR_Hpol_sorted_temp[ii];
-      
+
       // for this mode, can get TDR_all_sorted from these two arrays:
     }
 
     /*
     if(settings1->TRIG_MODE==2){
-     
+
       if(N_pass_0>=settings1->N_TRIG_0) for(int ii=0;ii<N_pass_0;ii++) if(TDR_Vpol_sorted_temp[ii]<stations[i].TDR_Vpol_sorted[ii]) stations[i].TDR_Vpol_sorted[ii]=TDR_Vpol_sorted_temp[ii];
       if(N_pass_1>=settings1->N_TRIG_1) for(int ii=0;ii<N_pass_1;ii++) if(TDR_Hpol_sorted_temp[ii]<stations[i].TDR_Hpol_sorted[ii]) stations[i].TDR_Hpol_sorted[ii]=TDR_Hpol_sorted_temp[ii];
-      
+
       // for this mode, can get TDR_all_sorted from these two arrays:
     }
     */
 
-    
+
     }// if trigger and buffer changed
-    
+
   }// while trig_i
-  
+
   if(scan_mode>1&&stations[i].Global_Pass){
-    
+
     if(settings1->TRIG_MODE==0){
-     
+
       cout<<"\nPthresh best: ";
       for(int ii=0;ii<3;ii++) cout<<" "<<stations[i].TDR_all_sorted[ii];
       cout<<"\n";
-        
+
       // debug output:
       if(stations[i].TDR_all_sorted[0]>stations[i].TDR_all_sorted[1]||stations[i].TDR_all_sorted[1]>stations[i].TDR_all_sorted[2]){
-	   
+
 	cout<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n  ordering problem: "<<stations[i].TDR_all_sorted[0]<<" "<<stations[i].TDR_all_sorted[1]<<" "<<stations[i].TDR_all_sorted[2]<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n";
-		
+
       }// ordering problem
-      
-   
+
+
     }// trig mode 0
-    
-    
+
+
     if(settings1->TRIG_MODE==1){
       cout<<"\nPthresh best: ";
       cout<<"  Vpol: "; for(int ii=0;ii<stations[i].TDR_Vpol_sorted.size();ii++) cout<<" "<<stations[i].TDR_Vpol_sorted[ii];
       cout<<"  Hpol: "; for(int ii=0;ii<stations[i].TDR_Hpol_sorted.size();ii++) cout<<" "<<stations[i].TDR_Hpol_sorted[ii];
       cout<<"\n";
-      
-        
+
+
       // debug output:
       if(stations[i].TDR_Vpol_sorted[0]>stations[i].TDR_Vpol_sorted[1]||stations[i].TDR_Vpol_sorted[1]>stations[i].TDR_Vpol_sorted[2]){
-	   
+
 	cout<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n  ordering problem (final) Vpol: "<<stations[i].TDR_Vpol_sorted[0]<<" "<<stations[i].TDR_Vpol_sorted[1]<<" "<<stations[i].TDR_Vpol_sorted[2]<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n";
-	
+
       }// ordering problem
-	  
+
       // debug output:
       if(stations[i].TDR_Hpol_sorted[0]>stations[i].TDR_Hpol_sorted[1]||stations[i].TDR_Hpol_sorted[1]>stations[i].TDR_Hpol_sorted[2]){
-	   
+
 	cout<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n  ordering problem (final), Hpol: "<<stations[i].TDR_Hpol_sorted[0]<<" "<<stations[i].TDR_Hpol_sorted[1]<<" "<<stations[i].TDR_Hpol_sorted[2]<<"\n";
 	for(int p=0;p<80;p++) cout<<"*";
 	cout<<"\n";
-		
+
       }// ordering problem
-         
+
     }// trig mode 1
-    
+
   }// if scan_mode>1 and global pass
-  
+
 
   for(int trig_j=0;trig_j<numChan; trig_j++) delete buffer[trig_j];
   delete [] buffer;
-  
+
   if(scan_mode>1){
-    
+
     delete [] TDR_all_sorted_temp;
     delete [] TDR_Vpol_sorted_temp;
     delete [] TDR_Hpol_sorted_temp;
   }
-  
-  
+
+
   return stations[i].Global_Pass;
-  
+
 }
 
 int Report::saveTriggeredEvent(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int last_trig_bin){
- 
+
   int i=stationID;
   int numChan=stations[i].TDR_all.size();
   cout<<"saving event"<<endl;
@@ -3378,71 +3465,71 @@ int Report::saveTriggeredEvent(Settings *settings1, Detector *detector, Event *e
 
 
   for(int trig_j=0; trig_j<numChan;trig_j++){
-    
+
     int string_i = detector->getStringfromArbAntID( i, trig_j);
     int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
-    
+
     if(stations[i].strings[string_i].antennas[antenna_i].Trig_Pass){// if this channel triggered
-    
+
     stations[i].strings[string_i].antennas[antenna_i].Likely_Sol = -1; // no likely init
-    
+
     int mindBin = 1.e9; // init big values
     int dBin = 0;
-    
+
     for (int m=0; m<stations[i].strings[string_i].antennas[antenna_i].ray_sol_cnt; m++) {   // loop over raysol numbers
 
       if ( stations[i].strings[string_i].antennas[antenna_i].SignalExt[m] ) {
 
 	dBin = abs( stations[i].strings[string_i].antennas[antenna_i].SignalBin[m] - stations[i].strings[string_i].antennas[antenna_i].Trig_Pass );
-               
+
 	if ( dBin < mindBin ) {
-    
+
 	  stations[i].strings[string_i].antennas[antenna_i].Likely_Sol = m; // store the ray sol number which is minimum difference between Trig_Pass bin
 	  mindBin = dBin;
-        	
+
 	}
       }
-      
-      
+
+
     }// for m (ray sol numbers)
-    
-    
-    
-    
-    
+
+
+
+
+
       if ( settings1->TRIG_ONLY_LOW_CH_ON==0 ) {
 
 	cout<<endl<<"trigger passed at bin "<<stations[i].strings[string_i].antennas[antenna_i].Trig_Pass<<"  passed ch : "<<trig_j<<" ("<<detector->stations[i].strings[string_i].antennas[antenna_i].type<<"type) Direct dist btw posnu : "<<event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[string_i].antennas[antenna_i] )<<" noiseID : "<<stations[i].strings[string_i].antennas[antenna_i].noise_ID[0];
-        
+
 	if (stations[i].strings[string_i].antennas[antenna_i].Likely_Sol != -1) {
-        
+
 	  cout<<" ViewAngle : "<<stations[i].strings[string_i].antennas[antenna_i].view_ang[0]*DEGRAD<<" LikelyTrigSignal : "<<stations[i].strings[string_i].antennas[antenna_i].Likely_Sol;
-        	  
+
 	}
       }
       else if ( settings1->TRIG_ONLY_LOW_CH_ON==1 ) {
-      
+
 	cout<<endl<<"trigger passed at bin "<<stations[i].strings[string_i].antennas[antenna_i].Trig_Pass<<"  passed ant: str["<<string_i<<"].ant["<<antenna_i<<"] ("<<detector->stations[i].strings[string_i].antennas[antenna_i].type<<"type) Direct dist btw posnu : "<<event->Nu_Interaction[0].posnu.Distance( detector->stations[i].strings[string_i].antennas[antenna_i] )<<" noiseID : "<<stations[i].strings[string_i].antennas[antenna_i].noise_ID[0];
-        
+
 	if (stations[i].strings[string_i].antennas[antenna_i].Likely_Sol != -1) {
-        
+
 	  cout<<" ViewAngle : "<<stations[i].strings[string_i].antennas[antenna_i].view_ang[0]*DEGRAD<<" LikelyTrigSignal : "<<stations[i].strings[string_i].antennas[antenna_i].Likely_Sol;
-          	  
+
 	}
-        
+
       }
-      
-      
 
-       
+
+
+
     }// if Trig_Pass
-      
+
 // now save the voltage waveform to V_mimic
       for (int mimicbin=0; mimicbin < waveformLength/2; mimicbin++) {
 
 	// new DAQ waveform writing mechanism test
         if (settings1->V_MIMIC_MODE == 0) { // Global passed bin is the center of the window
-        
+
 	  stations[i].strings[string_i].antennas[antenna_i].V_mimic.push_back( ( trigger->Full_window_V[trig_j][ last_trig_bin - waveformLength/2 + waveformCenter + mimicbin ] )*1.e3 );// save in mV
           stations[i].strings[string_i].antennas[antenna_i].time.push_back(  last_trig_bin - waveformLength/2 + waveformCenter + mimicbin );
           stations[i].strings[string_i].antennas[antenna_i].time_mimic.push_back( ( waveformLength/2 + waveformCenter + mimicbin) * settings1->TIMESTEP*1.e9  );// save in ns
@@ -3451,20 +3538,20 @@ int Report::saveTriggeredEvent(Settings *settings1, Detector *detector, Event *e
           stations[i].strings[string_i].antennas[antenna_i].V_mimic.push_back( ( trigger->Full_window_V[trig_j][  last_trig_bin - (detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin) - waveformLength/2 + waveformCenter + mimicbin ] )*1.e3 );// save in mV
           stations[i].strings[string_i].antennas[antenna_i].time.push_back(  last_trig_bin - (detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin) - waveformLength/2 + waveformCenter + mimicbin );
           stations[i].strings[string_i].antennas[antenna_i].time_mimic.push_back( ( -(detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin) - waveformLength/2 + waveformCenter + mimicbin) * settings1->TIMESTEP*1.e9  );// save in ns
-          	  
+
 	}
-          
+
           else if (settings1->V_MIMIC_MODE == 2) { // Global passed bin is the center of the window + delay to each chs from araGeom + fitted by eye
-          
+
            stations[i].strings[string_i].antennas[antenna_i].V_mimic.push_back( ( trigger->Full_window_V[trig_j][  last_trig_bin - (detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin + detector->stations[i].strings[string_i].antennas[antenna_i].manual_delay_bin) - waveformLength/2 + waveformCenter + mimicbin ] )*1.e3 );// save in mV
 	   stations[i].strings[string_i].antennas[antenna_i].time.push_back(  last_trig_bin - (detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin + detector->stations[i].strings[string_i].antennas[antenna_i].manual_delay_bin) - waveformLength/2 + waveformCenter + mimicbin );
            stations[i].strings[string_i].antennas[antenna_i].time_mimic.push_back( ( -(detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin + detector->stations[i].strings[string_i].antennas[antenna_i].manual_delay_bin) - waveformLength/2 + waveformCenter + mimicbin) * settings1->TIMESTEP*1.e9 + detector->params.TestBed_WFtime_offset_ns );// save in ns
-           	    
+
 	  }
-        	
+
       }
-      
-            
+
+
       // set global_trig_bin values
        if (settings1->V_MIMIC_MODE == 0) { // Global passed bin is the center of the window
          stations[i].strings[string_i].antennas[antenna_i].global_trig_bin = waveformLength/2 + waveformCenter ;
@@ -3475,65 +3562,65 @@ int Report::saveTriggeredEvent(Settings *settings1, Detector *detector, Event *e
        else if (settings1->V_MIMIC_MODE == 2) { // Global passed bin is the center of the window + delay to each chs from araGeom + fitted by eye
           stations[i].strings[string_i].antennas[antenna_i].global_trig_bin = (detector->params.TestBed_Ch_delay_bin[trig_j] - detector->params.TestBed_BH_Mean_delay_bin + detector->stations[i].strings[string_i].antennas[antenna_i].manual_delay_bin) + waveformLength/2 + waveformCenter ;
        }
-      
-      
+
+
       double arrivtime = stations[i].strings[string_i].antennas[antenna_i].arrival_time[0];
       double X = detector->stations[i].strings[string_i].antennas[antenna_i].GetX();
       double Y = detector->stations[i].strings[string_i].antennas[antenna_i].GetY();
       double Z = detector->stations[i].strings[string_i].antennas[antenna_i].GetZ();
-      
-      
+
+
       stations[i].total_trig_search_bin = stations[i].Global_Pass + trig_window_bin - trig_search_init;
-      
-      
-      
-      
-      
-      
-      
-    
+
+
+
+
+
+
+
+
   }// for trig_j
-  
-  
+
+
    if(settings1->OUTPUT_TDR_GRAPH>0){
-     
+
      settings1->OUTPUT_TDR_GRAPH--;
-     
+
      TGraph **gr=new TGraph*[numChan];
-     
+
      for(int trig_j=0;trig_j<numChan;trig_j++){
-      
+
        int string_i = detector->getStringfromArbAntID( i, trig_j);
        int antenna_i = detector->getAntennafromArbAntID( i, trig_j);
        int channel_num = detector->GetChannelfromStringAntenna ( i, string_i, antenna_i, settings1 );
        double thresh_value=0;
-       
-      // assign Pthresh a value 
+
+      // assign Pthresh a value
       if(settings1->NOISE_CHANNEL_MODE==0) thresh_value=detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode * detector->GetThresOffset( i, channel_num-1,settings1);
       if(settings1->NOISE_CHANNEL_MODE==1) thresh_value=detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1);
       if(settings1->NOISE_CHANNEL_MODE==2){
-	  
+
 	  if(channel_num-1 < 8) thresh_value=detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode_ch[channel_num-1] * detector->GetThresOffset( i, channel_num-1,settings1);
 	  else thresh_value=detector->GetThres(i, channel_num-1, settings1) * trigger->rmsdiode_ch[8] * detector->GetThresOffset( i, channel_num-1,settings1);
-	  
+
 	}
-       
+
        gr[trig_j]=new TGraph();
        for(int trig_i=0;trig_i<settings1->DATA_BIN_SIZE/2;trig_i++) gr[trig_j]->SetPoint(trig_i, (trig_search_init+trig_i), trigger->Full_window[trig_j][trig_i]);
        gr[trig_j]->SetNameTitle(Form("TDR_waveform%dC%02d",  settings1->OUTPUT_TDR_GRAPH, trig_j), Form("Tunnel diode response waveform %d, channel %02d, trig_pass= %d, P_{th}= %le; time bins; power after convolution with tunnel diode", settings1->OUTPUT_TDR_GRAPH, trig_j, stations[i].strings[string_i].antennas[antenna_i].Trig_Pass, thresh_value));
        gr[trig_j]->Write();
        delete gr[trig_j];
      }
-     
+
      delete [] gr;
-     
-	
+
+
    }
-  
+
   return 1;
-  
-  
-  
+
+
+
 }// saveTriggeredEvent
 
 #ifdef ARA_UTIL_EXISTS
@@ -3553,11 +3640,11 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
             int antenna_i = detector->getAntennafromArbAntID( stationIndex, ch_loop);
             int AraRootChannel = 0;
             AraRootChannel = detector->GetChannelfromStringAntenna (i, string_i, antenna_i, settings1);
-            
+
             int UsefulEventBin;
             if ( settings1->NFOUR/2 < EFFECTIVE_LAB3_SAMPLES*2) UsefulEventBin = settings1->NFOUR/2;
             else UsefulEventBin = EFFECTIVE_LAB3_SAMPLES*2;
-            
+
             //for (int mimicbin=0; mimicbin<settings1->NFOUR/2; mimicbin++) {
             for (int mimicbin=0; mimicbin<UsefulEventBin; mimicbin++) {
                 if (stations[stationIndex].Global_Pass > 0){
@@ -3584,9 +3671,9 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
 	cout << "StationID: " << stationID << endl;
 	theUsefulEvent->fNumChannels = 32;
 	theUsefulEvent->stationId = stationID;
-	
+
 	//	cout << endl << stationID << endl;
-	
+
 	int ch_limit;
 	if (stationID == 0){
 	  ch_limit = 14;
@@ -3595,7 +3682,7 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
 	}
 
 	int maxElecChans = 32;
-	
+
 	for (int ch_loop=0; ch_loop < ch_limit; ch_loop++) {
 	  //	  int elecChan = AraGeom->getElecChanFromRFChan(ch_loop, stationID);
 	  int elecChan = AraGeomTool::Instance()->getElecChanFromRFChan(ch_loop, stationID);
@@ -3609,7 +3696,7 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
 	  //	  int antenna_i = detector->getAntennafromArbAntID( stationIndex, ch_loop);
 	  int AraRootChannel = 0;
 	  AraRootChannel = detector->GetChannelfromStringAntenna (stationID, string_i, antenna_i, settings1);
-	  
+
 	  int UsefulEventBin;
 	  //	  if ( settings1->NFOUR/2 < EFFECTIVE_LAB3_SAMPLES*2) UsefulEventBin = settings1->NFOUR/2;
 	  //	  else UsefulEventBin = EFFECTIVE_LAB3_SAMPLES*2;
@@ -3624,15 +3711,15 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
 	  //	  theUsefulEvent->fVolts[AraRootChannel-1].resize(UsefulEventBin);
 	  //	  theUsefulEvent->fTimes[AraRootChannel-1].resize(UsefulEventBin);
 	  //	  cout << string_i << " : " << antenna_i << endl;
-	  
+
 	  //for (int mimicbin=0; mimicbin<settings1->NFOUR/2; mimicbin++) {
 	  for (int mimicbin=0; mimicbin<UsefulEventBin; mimicbin++) {
 	    if (stations[stationIndex].Global_Pass > 0){
 	      //	      cout << "Test 1" << endl;
 	      volts[mimicbin] = stations[stationIndex].strings[string_i].antennas[antenna_i].V_mimic[mimicbin];
 	      times[mimicbin] = stations[stationIndex].strings[string_i].antennas[antenna_i].time_mimic[mimicbin];
-	      
-	      
+
+
 	    }
 	    else {
 	      volts[mimicbin] = 0.;
@@ -3656,7 +3743,7 @@ void Report::MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *t
 
 
 void Report::ClearUselessfromConnect(Detector *detector, Settings *settings1, Trigger *trigger){
-    
+
     for (int i = 0; i< detector->params.number_of_stations; i++) {
         // now remove all information which are useless
         for (int c_j=0; c_j< detector->stations[i].strings.size(); c_j++) {
@@ -3680,15 +3767,15 @@ void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger,
 //    int BINSIZE = detector->stations[StationIndex].NFOUR/2;
     int bin_value;
     //vector <double> V_total_forconvlv;   // total time domain waveform (noise + signal)
-    
+
     V_total_forconvlv.clear();
-    
+
     // first, fill the noise values
     for (int bin=0; bin<BINSIZE; bin++) {   //BINSIZE should be NFOUR/2
         bin_value = signalbin - BINSIZE/2 + bin;
 
         // save the noise + signal waveform
-                           
+
         if ( settings1->NOISE_CHANNEL_MODE==0) {
             V_total_forconvlv.push_back( trigger->v_noise_timedomain[ noise_ID[ (int)( bin_value / settings1->DATA_BIN_SIZE) ] ][ (int)( bin_value % settings1->DATA_BIN_SIZE ) ]  + V[bin] );
         }
@@ -3734,7 +3821,7 @@ void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger,
 
 
 
-// this one is for two connected signals 
+// this one is for two connected signals
 void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin1, int signalbin2, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex) {
 
     int BINSIZE = settings1->NFOUR/2;
@@ -3747,9 +3834,9 @@ void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger,
     for(int bin_tmp=0; bin_tmp<BINSIZE*2; bin_tmp++) {
         V_tmp[bin_tmp] = 0.;
     }
-    
+
     V_total_forconvlv.clear();
-    
+
     // first, fill the noise values
     for (int bin=0; bin<BINSIZE*2; bin++) {
         bin_value = signalbin1 - BINSIZE/2 + bin;
@@ -3812,7 +3899,7 @@ void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger,
 
 
 
-// this one is for three connected signals 
+// this one is for three connected signals
 void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin0, int signalbin1, int signalbin2, vector <double> &V0, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex) {
 
     int BINSIZE = settings1->NFOUR/2;
@@ -3826,9 +3913,9 @@ void Report::Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger,
     for(int bin_tmp=0; bin_tmp<BINSIZE*2; bin_tmp++) {
         V_tmp[bin_tmp] = 0.;
     }
-    
+
     V_total_forconvlv.clear();
-    
+
     // first, fill the noise values
     for (int bin=0; bin<BINSIZE*2; bin++) {
         bin_value = signalbin1 - BINSIZE/2 + bin;
@@ -3914,7 +4001,7 @@ void Report::Apply_Gain_Offset(Settings *settings1, Trigger *trigger, Detector *
     //cout<<"station "<<StationIndex<<" ch"<<channel_num<<" applying gain offset "<<detector->GetGainOffset( StationIndex, channel_num, settings1 )<<" applying"<<endl;
 
     for (int bin=0; bin<settings1->DATA_BIN_SIZE; bin++) {   // test for full window
-        
+
         trigger->Full_window[ID][bin] = ( trigger->Full_window[ID][bin] * detector->GetGainOffset( StationIndex, channel_num-1, settings1 ) * detector->GetGainOffset( StationIndex, channel_num-1, settings1 ) ); // offset in voltage factor so we need power (V^2 factor to diode response)
         trigger->Full_window_V[ID][bin] = ( trigger->Full_window_V[ID][bin] * detector->GetGainOffset( StationIndex, channel_num-1, settings1 ) ); // gain in voltage factor
     }
@@ -3927,13 +4014,13 @@ int Report::GetChNumFromArbChID( Detector *detector, int ID, int StationIndex, S
 
     int string_num = detector->getStringfromArbAntID( StationIndex, ID );
     int ant_num = detector->getAntennafromArbAntID( StationIndex, ID );
-    
+
     int StationID = detector->stations[StationIndex].StationID;
     //    cout << "Station ID: " << StationID << endl;
     //    cout << "string_num: " << string_num << endl;
     //    cout << "ant_num: " << ant_num << endl;
     //    cout << StationID << " : " << string_num << " : " << ant_num << endl;
-    
+
     //int channel_num = detector->GetChannelfromStringAntenna ( StationIndex, string_num, ant_num );
     int channel_num = detector->GetChannelfromStringAntenna ( StationID, string_num, ant_num, settings1 );
 
@@ -3948,21 +4035,21 @@ Vector Report::GetPolarization (Vector &nnu, Vector &launch_vector) {
     // Want to find a unit vector in the same plane as
     // nnu and launch_vector, but perpendicular to launch_vector, pointing away
     // from nnu.
-    
+
     // cross nnu with launch_vector to get the direction of the B field.
     Vector n_bfield = nnu.Cross(launch_vector);
-    
+
     // cross b-field with nrf2_iceside to get the polarization vector.
     Vector n_pol = n_bfield.Cross(launch_vector);
-    
+
     n_pol = n_pol.Unit();
-    
+
     // check and make sure E-field is pointing in the right direction.
     if (nnu*launch_vector>0 && n_pol*nnu>0)
 	cout << "error in GetPolarization.  \n";
-    
-    
-    
+
+
+
     return n_pol;
 } //GetPolarization
 
@@ -3993,7 +4080,7 @@ double Report::GaintoHeight(double gain, double freq, double n_medium) {
     // from gain=4*pi*A_eff/lambda^2
     // and h_eff=2*sqrt(A_eff*Z_rx/Z_air)
     // gain is unitless value
-    
+
     return 2*sqrt(gain/4/PI*CLIGHT*CLIGHT/(freq*freq*n_medium*n_medium)*Zr/(Z0/n_medium));  // n_medium parts are changed from icemc(I believe this is correct one; E. Hong)
 }
 
@@ -4340,35 +4427,35 @@ void Report::ApplyRFCM_databin(int ch, int bin_n, Detector *detector, double &vm
 void Report::ApplyNoiseFig_databin(int ch, int bin_n, Detector *detector, double &vmmhz, Settings *settings1) {  // read noise figure and apply unitless gain to vmmhz
   //cout<<"Entered ApplyNoiseFig_databin    ";
   //cout<<"vmmhz: "<<vmmhz;
-  
+
   double tempNoise = vmmhz*vmmhz;
   //  cout<<"    1: "<<detector->GetNoiseFig_databin(ch,bin_n);
   //  cout<<"    2: "<<detector->GetTransm_databin(ch, bin_n);
   //  cout<<"    3: "<<settings1->NOISE_TEMP;
   //FILE *fp = fopen("noiseTemp_NOISE_CHANNEL_MODE_0.txt","a+");
-  if(detector->GetNoiseFig_databin(ch,bin_n)>1.0){vmmhz = TMath::Sqrt( tempNoise*(detector->GetTransm_databin(ch, bin_n)) + tempNoise/(settings1->NOISE_TEMP)*220.0*(detector->GetNoiseFig_databin(ch,bin_n) - 1.0) ) ;  
+  if(detector->GetNoiseFig_databin(ch,bin_n)>1.0){vmmhz = TMath::Sqrt( tempNoise*(detector->GetTransm_databin(ch, bin_n)) + tempNoise/(settings1->NOISE_TEMP)*220.0*(detector->GetNoiseFig_databin(ch,bin_n) - 1.0) ) ;
     //cout<<"   vmmhz   "<<vmmhz;
-    //cout<<"   bin: "<<bin_n<<" freq: "<<detector->GetFreq(bin_n) << " noise temp: " << 246.0*((detector->GetTransm_databin(ch, bin_n)) + 1.0/(settings1->NOISE_TEMP)*220.0*(detector->GetNoiseFig_databin(ch,bin_n) - 1.0) ) << endl;  
+    //cout<<"   bin: "<<bin_n<<" freq: "<<detector->GetFreq(bin_n) << " noise temp: " << 246.0*((detector->GetTransm_databin(ch, bin_n)) + 1.0/(settings1->NOISE_TEMP)*220.0*(detector->GetNoiseFig_databin(ch,bin_n) - 1.0) ) << endl;
     //fprintf(fp, "%f   ",246.0*((detector->GetTransm_databin(ch, bin_n)) + 1.0/(settings1->NOISE_TEMP)*220.0*(detector->GetNoiseFig_databin(ch,bin_n) - 1.0) ));
 }
   else{
     vmmhz = vmmhz;
     //fprintf(fp, "%f   ",246.0);
   }
-  
+
   //fclose(fp);
   //    if(ch==0 && bin_n==2050) cout << "Noise ch: "<< ch <<"   "<< detector->GetNoiseFig_databin(ch,bin_n) << "   " << detector->GetTransm_databin(ch, bin_n)
 //		<< "   " << TMath::Sqrt( tempNoise ) << "   " << vmmhz << endl;
   //  if(ch==8 && bin_n==2050) cout << "Noise ch: "<< ch <<"   "<< detector->GetNoiseFig_databin(ch,bin_n) << "   " << detector->GetTransm_databin(ch, bin_n)
   //		<< "   " << TMath::Sqrt( tempNoise ) << "   " << vmmhz << endl;
   //    if(ch==24 && bin_n==2000) cout << "Noise ch: "<< ch << "   " << detector->GetNoiseFig_databin(ch,bin_n)*220.0/246.0 << "   " << TMath::Sqrt(detector->GetTransm_databin(ch, bin_n) ) << endl;
-  
+
 }
 
 
 
 
-void Report::GetAngleAnt(Vector &rec_vector, Position &antenna, double &ant_theta, double &ant_phi) {   //ant_theta and ant_phi is in degree 
+void Report::GetAngleAnt(Vector &rec_vector, Position &antenna, double &ant_theta, double &ant_phi) {   //ant_theta and ant_phi is in degree
 
     // need to fix some parts.
     // currently phi is not correct.
@@ -4397,7 +4484,7 @@ void Report::GetAngleAnt(Vector &rec_vector, Position &antenna, double &ant_thet
 void Report::GetNoiseWaveforms(Settings *settings1, Detector *detector, double v_noise, double *vnoise) {
 
     if (settings1->NOISE == 0) {    // NOISE == 0 : flat thermal noise with Johnson-Nyquist noise
-        //V_noise_fft_bin = sqrt( (double)(NFOUR/2) * 50. * KBOLTZ * T_noise / (2. * TIMESTEP) ); 
+        //V_noise_fft_bin = sqrt( (double)(NFOUR/2) * 50. * KBOLTZ * T_noise / (2. * TIMESTEP) );
 
         Vfft_noise_after.clear();  // remove previous Vfft_noise values
         Vfft_noise_before.clear();  // remove previous Vfft_noise values
@@ -4452,7 +4539,7 @@ void Report::GetNoiseWaveforms(Settings *settings1, Detector *detector, double v
 
            //vnoise[2 * k] = (V_tmp) * cos(noise_phase[k]);
            //vnoise[2 * k + 1] = (V_tmp) * sin(noise_phase[k]);
-           
+
 
             Vfft_noise_after.push_back( vnoise[2*k] );
             Vfft_noise_after.push_back( vnoise[2*k+1] );
@@ -4468,7 +4555,7 @@ void Report::GetNoiseWaveforms(Settings *settings1, Detector *detector, double v
         // now vnoise is time domain waveform
         Tools::realft( vnoise, -1, settings1->DATA_BIN_SIZE);
 
-        
+
         // save timedomain noise to Report class
         /*
         for (int k=0; k<settings1->DATA_BIN_SIZE; k++) {
@@ -4522,7 +4609,7 @@ void Report::GetNoiseWaveforms_ch(Settings *settings1, Detector *detector, doubl
 
 
             Vfft_noise_before.push_back( V_tmp );
-	    
+
 
             current_phase = noise_phase[k];
 
@@ -4551,7 +4638,7 @@ void Report::GetNoiseWaveforms_ch(Settings *settings1, Detector *detector, doubl
         // now vnoise is time domain waveform
         Tools::realft( vnoise, -1, settings1->DATA_BIN_SIZE);
 
-        
+
         // save timedomain noise to Report class
         /*
         for (int k=0; k<settings1->DATA_BIN_SIZE; k++) {
@@ -4639,7 +4726,7 @@ void Report::GetNoiseWaveforms_ch(Settings *settings1, Detector *detector, doubl
         // now vnoise is time domain waveform
         Tools::realft( vnoise, -1, settings1->DATA_BIN_SIZE);
 
-        
+
         // save timedomain noise to Report class
         /*
         for (int k=0; k<settings1->DATA_BIN_SIZE; k++) {
@@ -4670,7 +4757,7 @@ void Report::GetNoisePhase(Settings *settings1) {
 }
 
 
-    
+
 
 void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int StationIndex, vector <double> &vsignal_array, double *vsignal_forfft) {
 
@@ -4683,7 +4770,7 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 //    int NFOUR = detector->stations[StationIndex].NFOUR;
 //    int TIMESTEP = detector->stations[StationIndex].TIMESTEP;
     Tools::Zero(vsignal_forfft,NFOUR/2);
-    
+
 
 
     if (settings1->AVZ_NORM_FACTOR_MODE == 0) { // use previous normalization factors
@@ -4697,41 +4784,41 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
         int ilastnonzero=2000;
         //for (int i=0;i<NFREQ;i++) {
         for (int i=0;i<detector->GetFreqBin();i++) {
-            
+
             // freq_forfft has NFOUR/2 elements because it is meant to cover real and imaginary values
             // but there are only NFOUR/4 different values
             // it's the index among the NFOUR/4 that we're interested in
             int ifour=Tools::Getifreq(detector->GetFreq(i),detector->freq_forfft[0],detector->freq_forfft[NFOUR/2-1],NFOUR/4);
-            
+
             if (ifour!=-1 && 2*ifour+1<NFOUR/2) {
                 count_nonzero++;
                 if (ifirstnonzero==-1)
                     ifirstnonzero=ifour;
-                
+
                 vsignal_forfft[2*ifour]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // inverse fft normalization factor (2/(N/2)), 1/dt for change integration fft form to discrete numerical fft
-                
+
                 //      cout << "ifour, vsignal is " << ifour << " " << vsignal_e_forfft[2*ifour] << "\n";
-                
+
                 vsignal_forfft[2*ifour+1]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // phase is 90 deg.
                 // the 2/(nfour/2) needs to be included since were using Tools::realft with the -1 setting
-                
+
                 // how about we interpolate instead of doing a box average
-                
+
                 for (int j=iprevious+1;j<ifour;j++) {
                     vsignal_forfft[2*j]=previous_value_e_even+(vsignal_forfft[2*ifour]-previous_value_e_even)*(double)(j-iprevious)/(double)(ifour-iprevious);
                     //	cout << "j, vsignal is " << j << " " << vsignal_e_forfft[2*j] << "\n";
-                    
+
                     vsignal_forfft[2*j+1]=previous_value_e_odd+(vsignal_forfft[2*ifour+1]-previous_value_e_odd)*(double)(j-iprevious)/(double)(ifour-iprevious);
                 }
-                
+
                 ilastnonzero=ifour;
                 iprevious=ifour;
                 previous_value_e_even=vsignal_forfft[2*ifour];
                 previous_value_e_odd=vsignal_forfft[2*ifour+1];
             }
-            
+
         } // end loop over nfreq
-        
+
 
 
         // don't applying any extra factor for the change in array (change of bin size)
@@ -4748,7 +4835,7 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
 
 
-        
+
         //  Tools::InterpolateComplex(vsignal_e_forfft,NFOUR/4);
         //Tools::InterpolateComplex(vsignal_h_forfft,NFOUR/4);
         for (int ifour=0;ifour<NFOUR/4;ifour++) {
@@ -4757,82 +4844,82 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
             vsignal_forfft[2*ifour]*=cos(settings1->PHASE*PI/180.);
             vsignal_forfft[2*ifour+1]*=sin(settings1->PHASE*PI/180.);
-            
+
             //--------------------------------------------------
             // if (!PULSER) {
-            //     
+            //
             //     vsignal_forfft[2*ifour]*=cos(phase*PI/180.);
             //     vsignal_forfft[2*ifour+1]*=sin(phase*PI/180.);
-            //     
-            //     
+            //
+            //
             // }
             // else {
             //     vsignal_forfft[2*ifour]*=cos(v_phases[ifour]*PI/180.);
             //     vsignal_forfft[2*ifour+1]*=sin(v_phases[ifour]*PI/180.);
-            //     
-            // }	  	  	  
-            //-------------------------------------------------- 
-            
-            
+            //
+            // }
+            //--------------------------------------------------
+
+
         }
     }
     else if (settings1->AVZ_NORM_FACTOR_MODE == 1) { // use new (fixed) normalization factors
-    
+
         double dF = 1. / ((double)(NFOUR/2) * TIMESTEP); // in Hz
         //cout<<"dF1 : "<<dF<<endl;
-            
+
         double dF_org = detector->GetFreq(1) - detector->GetFreq(0); // in Hz
-            
+
         //double dF_factor = sqrt( dF_org / dF );
          double dF_factor = 1.;
          //double dF_factor = sqrt( dF / dF_org );
-            
+
          int Norg = detector->GetFreqBin();
-                                    
+
          double FreqOrg[Norg+1];
          double VmMHzOrg[Norg+1];
-                                            
+
          double FreqNFOUR[NFOUR/4+1]; // one more bin
          double VmMHzNFOUR[NFOUR/4+1]; // one more bin
-         
+
          for (int i=0;i<Norg+1;i++) {
-                                                        
+
              if ( i==0 ) {
-                                                                       
+
                  VmMHzOrg[i] = 0.;
                  FreqOrg[i] = 0.;
              }
              else {
-                                                                                                              
+
                  VmMHzOrg[i] = vsignal_array[i-1];
                  FreqOrg[i] = detector->GetFreq(i-1);
              }
-                                                                                                                                      
+
          }
-                                                                                                                                          
+
          for (int ifour=0;ifour<NFOUR/4+1;ifour++) {
-                                                                                                                                                   
+
              FreqNFOUR[ifour] = dF * (double)ifour;
              VmMHzNFOUR[ifour] = 0.;
-                                                                                                                                                                
+
          }
-         
-           
+
+
          //Tools::SimpleLinearInterpolation_OutZero( Norg, FreqOrg, vsignal_array, NFOUR/4+1, FreqNFOUR, VmMHzNFOUR );
          Tools::SimpleLinearInterpolation_OutZero( Norg+1, FreqOrg, VmMHzOrg, NFOUR/4+1, FreqNFOUR, VmMHzNFOUR );
-          
-           
+
+
          for (int ifour=1;ifour<NFOUR/4;ifour++) {
-           
+
              // same amplitude, 2/(NFOUR/2) for inverse FFT normalization factor
              vsignal_forfft[2*ifour] = VmMHzNFOUR[ifour] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP; // change to V/Hz, apply norm factor, change to Hn
              vsignal_forfft[2*ifour+1] = VmMHzNFOUR[ifour] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
-          
+
              // apply phase
              vsignal_forfft[2*ifour]*=cos(settings1->PHASE*PI/180.);
              vsignal_forfft[2*ifour+1]*=sin(settings1->PHASE*PI/180.);
          }
-           
+
          // first and last freq bin read values to 0, 1 bin
          vsignal_forfft[0] = VmMHzNFOUR[0] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
          vsignal_forfft[1] = VmMHzNFOUR[NFOUR/4] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
@@ -4840,7 +4927,7 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
 
 
-    
+
 }
 
 
@@ -4861,7 +4948,7 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
     if (settings1->AVZ_NORM_FACTOR_MODE == 0) { // use previous normalization factors
 
-    
+
         double previous_value_e_even=0.;
         double previous_value_e_odd=0.;
         int count_nonzero=0;
@@ -4870,41 +4957,41 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
         int ilastnonzero=2000;
         //for (int i=0;i<NFREQ;i++) {
         for (int i=0;i<detector->GetFreqBin();i++) {
-            
+
             // freq_forfft has NFOUR/2 elements because it is meant to cover real and imaginary values
             // but there are only NFOUR/4 different values
             // it's the index among the NFOUR/4 that we're interested in
             int ifour=Tools::Getifreq(detector->GetFreq(i),detector->freq_forfft[0],detector->freq_forfft[NFOUR/2-1],NFOUR/4);
-            
+
             if (ifour!=-1 && 2*ifour+1<NFOUR/2) {
                 count_nonzero++;
                 if (ifirstnonzero==-1)
                     ifirstnonzero=ifour;
-                
+
                 vsignal_forfft[2*ifour]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // inverse fft normalization factor (2/(N/2)), 1/dt for change integration fft form to discrete numerical fft
-                
+
                 //      cout << "ifour, vsignal is " << ifour << " " << vsignal_e_forfft[2*ifour] << "\n";
-                
+
                 vsignal_forfft[2*ifour+1]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // phase is 90 deg.
                 // the 2/(nfour/2) needs to be included since were using Tools::realft with the -1 setting
-                
+
                 // how about we interpolate instead of doing a box average
-                
+
                 for (int j=iprevious+1;j<ifour;j++) {
                     vsignal_forfft[2*j]=previous_value_e_even+(vsignal_forfft[2*ifour]-previous_value_e_even)*(double)(j-iprevious)/(double)(ifour-iprevious);
                     //	cout << "j, vsignal is " << j << " " << vsignal_e_forfft[2*j] << "\n";
-                    
+
                     vsignal_forfft[2*j+1]=previous_value_e_odd+(vsignal_forfft[2*ifour+1]-previous_value_e_odd)*(double)(j-iprevious)/(double)(ifour-iprevious);
                 }
-                
+
                 ilastnonzero=ifour;
                 iprevious=ifour;
                 previous_value_e_even=vsignal_forfft[2*ifour];
                 previous_value_e_odd=vsignal_forfft[2*ifour+1];
             }
-            
+
         } // end loop over nfreq
-        
+
 
 
         // don't applying any extra factor for the change in array (change of bin size)
@@ -4921,7 +5008,7 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
 
 
-        
+
         //  Tools::InterpolateComplex(vsignal_e_forfft,NFOUR/4);
         //Tools::InterpolateComplex(vsignal_h_forfft,NFOUR/4);
         for (int ifour=0;ifour<NFOUR/4;ifour++) {
@@ -4930,82 +5017,82 @@ void Report::MakeArraysforFFT(Settings *settings1, Detector *detector, int Stati
 
             vsignal_forfft[2*ifour]*=cos(settings1->PHASE*PI/180.);
             vsignal_forfft[2*ifour+1]*=sin(settings1->PHASE*PI/180.);
-            
+
             //--------------------------------------------------
             // if (!PULSER) {
-            //     
+            //
             //     vsignal_forfft[2*ifour]*=cos(phase*PI/180.);
             //     vsignal_forfft[2*ifour+1]*=sin(phase*PI/180.);
-            //     
-            //     
+            //
+            //
             // }
             // else {
             //     vsignal_forfft[2*ifour]*=cos(v_phases[ifour]*PI/180.);
             //     vsignal_forfft[2*ifour+1]*=sin(v_phases[ifour]*PI/180.);
-            //     
-            // }	  	  	  
-            //-------------------------------------------------- 
-            
-            
+            //
+            // }
+            //--------------------------------------------------
+
+
         }
     }
     else if (settings1->AVZ_NORM_FACTOR_MODE == 1) { // use new (fixed) normalization factors
-    
+
         double dF = 1. / ((double)(NFOUR/2) * TIMESTEP); // in Hz
         //cout<<"dF1 : "<<dF<<endl;
-            
+
         double dF_org = detector->GetFreq(1) - detector->GetFreq(0); // in Hz
-            
+
         //double dF_factor = sqrt( dF_org / dF );
          double dF_factor = 1.;
          //double dF_factor = sqrt( dF / dF_org );
-            
+
          int Norg = detector->GetFreqBin();
-                                    
+
          double FreqOrg[Norg+1];
          double VmMHzOrg[Norg+1];
-                                            
+
          double FreqNFOUR[NFOUR/4+1]; // one more bin
          double VmMHzNFOUR[NFOUR/4+1]; // one more bin
-         
+
          for (int i=0;i<Norg+1;i++) {
-                                                        
+
              if ( i==0 ) {
-                                                                       
+
                  VmMHzOrg[i] = 0.;
                  FreqOrg[i] = 0.;
              }
              else {
-                                                                                                              
+
                  VmMHzOrg[i] = vsignal_array[i-1];
                  FreqOrg[i] = detector->GetFreq(i-1);
              }
-                                                                                                                                      
+
          }
-                                                                                                                                          
+
          for (int ifour=0;ifour<NFOUR/4+1;ifour++) {
-                                                                                                                                                   
+
              FreqNFOUR[ifour] = dF * (double)ifour;
              VmMHzNFOUR[ifour] = 0.;
-                                                                                                                                                                
+
          }
-         
-           
+
+
          //Tools::SimpleLinearInterpolation_OutZero( Norg, FreqOrg, vsignal_array, NFOUR/4+1, FreqNFOUR, VmMHzNFOUR );
          Tools::SimpleLinearInterpolation_OutZero( Norg+1, FreqOrg, VmMHzOrg, NFOUR/4+1, FreqNFOUR, VmMHzNFOUR );
-          
-           
+
+
          for (int ifour=1;ifour<NFOUR/4;ifour++) {
-           
+
              // same amplitude, 2/(NFOUR/2) for inverse FFT normalization factor
              vsignal_forfft[2*ifour] = VmMHzNFOUR[ifour] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP; // change to V/Hz, apply norm factor, change to Hn
              vsignal_forfft[2*ifour+1] = VmMHzNFOUR[ifour] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
-          
+
              // apply phase
              vsignal_forfft[2*ifour]*=cos(settings1->PHASE*PI/180.);
              vsignal_forfft[2*ifour+1]*=sin(settings1->PHASE*PI/180.);
          }
-           
+
          // first and last freq bin read values to 0, 1 bin
          vsignal_forfft[0] = VmMHzNFOUR[0] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
          vsignal_forfft[1] = VmMHzNFOUR[NFOUR/4] * 2/((double)NFOUR/2) * dF_factor / TIMESTEP;
@@ -5030,9 +5117,9 @@ void Report::MakeArraysforFFT_noise(Settings *settings1, Detector *detector, int
 
 //    int NFOUR = detector->stations[StationIndex].NFOUR;
 //    int TIMESTEP = detector->stations[StationIndex].TIMESTEP;
-    
+
     Tools::Zero(vsignal_forfft,NFOUR/2);
-    
+
     double previous_value_e_even=0.;
     double previous_value_e_odd=0.;
     int count_nonzero=0;
@@ -5041,41 +5128,41 @@ void Report::MakeArraysforFFT_noise(Settings *settings1, Detector *detector, int
     int ilastnonzero=2000;
     //for (int i=0;i<NFREQ;i++) {
     for (int i=0;i<detector->GetFreqBin();i++) {
-	
+
 	// freq_forfft has NFOUR/2 elements because it is meant to cover real and imaginary values
 	// but there are only NFOUR/4 different values
 	// it's the index among the NFOUR/4 that we're interested in
 	int ifour=Tools::Getifreq(detector->GetFreq(i),detector->freq_forfft[0],detector->freq_forfft[NFOUR/2-1],NFOUR/4);
-	
+
 	if (ifour!=-1 && 2*ifour+1<NFOUR/2) {
 	    count_nonzero++;
 	    if (ifirstnonzero==-1)
 		ifirstnonzero=ifour;
-	    
+
 	    vsignal_forfft[2*ifour]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // inverse fft normalization factor (2/(N/2)), 1/dt for change integration fft form to discrete numerical fft
-	    
+
 	    //      cout << "ifour, vsignal is " << ifour << " " << vsignal_e_forfft[2*ifour] << "\n";
-	    
+
 	    vsignal_forfft[2*ifour+1]=vsignal_array[i]*2/((double)NFOUR/2)/(TIMESTEP); // phase is 90 deg.
 	    // the 2/(nfour/2) needs to be included since were using Tools::realft with the -1 setting
-	    
+
 	    // how about we interpolate instead of doing a box average
-	    
+
 	    for (int j=iprevious+1;j<ifour;j++) {
 		vsignal_forfft[2*j]=previous_value_e_even+(vsignal_forfft[2*ifour]-previous_value_e_even)*(double)(j-iprevious)/(double)(ifour-iprevious);
 		//	cout << "j, vsignal is " << j << " " << vsignal_e_forfft[2*j] << "\n";
-		
+
 		vsignal_forfft[2*j+1]=previous_value_e_odd+(vsignal_forfft[2*ifour+1]-previous_value_e_odd)*(double)(j-iprevious)/(double)(ifour-iprevious);
 	    }
-	    
+
 	    ilastnonzero=ifour;
 	    iprevious=ifour;
 	    previous_value_e_even=vsignal_forfft[2*ifour];
 	    previous_value_e_odd=vsignal_forfft[2*ifour+1];
 	}
-	
+
     } // end loop over nfreq
-    
+
 
 
     // don't applying any extra factor for the change in array (change of bin size)
@@ -5093,13 +5180,13 @@ void Report::MakeArraysforFFT_noise(Settings *settings1, Detector *detector, int
 
     // phase for noise will be applied in GetNoiseWaveforms
 
-    
+
 }
 
 
 
 
-                                       
+
 
 
 
@@ -5260,161 +5347,159 @@ int Report::GetChannelNum8_LowAnt(int string_num, int antenna_num) {
 
 }
 
-                        
 
 
-                        
+
+
 
 TGraph *Report::getWaveform(Detector *detector, int ch, int station_i, int event_num, int run_num){
- 
+
   int string_i = detector->getStringfromArbAntID( station_i, ch);
   int antenna_i = detector->getAntennafromArbAntID( station_i, ch);
-  
+
   TGraph *gr=new TGraph();
-  
+
   int N=stations[station_i].strings[string_i].antennas[antenna_i].V_mimic.size();
-  
+
   for(int i=0;i<N;i++){
-   
+
     gr->SetPoint(i,stations[station_i].strings[string_i].antennas[antenna_i].time_mimic[i], stations[station_i].strings[string_i].antennas[antenna_i].V_mimic[i]);
-    
+
   }// for i
-  
+
   gr->SetNameTitle(Form("WF%dS%02dC%02d", event_num, station_i, ch), Form("Simulated waveform %d, station %d, channel %d;time (ns); voltage (mV)", event_num, station_i, ch));
-  
+
   return gr;
-  
+
 }
 
 
 vector<TGraph*> Report::getWaveformVector(Detector *detector, int station_i, int event_num, int run_num){
 
   vector<TGraph*> waveforms;
-  
+
   for(int ch=0;ch<detector->stations[station_i].number_of_antennas; ch++){
-      
+
     int string_i = detector->getStringfromArbAntID( station_i, ch);
     int antenna_i = detector->getAntennafromArbAntID( station_i, ch);
-    
+
     TGraph *gr=new TGraph();
-      
+
     int N=stations[station_i].strings[string_i].antennas[antenna_i].V_mimic.size();
-    
+
     for(int i=0;i<N;i++){
-   
+
       gr->SetPoint(i,stations[station_i].strings[string_i].antennas[antenna_i].time_mimic[i], stations[station_i].strings[string_i].antennas[antenna_i].V_mimic[i]);
-    
+
     }// for i
-  
+
     gr->SetNameTitle(Form("WF%dS%02dC%02d", event_num, station_i, ch), Form("Simulated waveform %d, station %d, channel %d;time (ns); voltage (mV)", event_num, station_i, ch));
-    
+
     waveforms.push_back(gr);
-    
+
   }// for ch
-  
+
   return waveforms;
-  
+
 }
 
 vector<TGraph*> Report::getWaveformVectorVpol(Detector *detector, int station_i, int event_num, int run_num){
- 
+
   vector<TGraph*> waveforms;
-  
+
   for(int ch=0;ch<detector->stations[station_i].number_of_antennas; ch++){
-      
+
     int string_i = detector->getStringfromArbAntID( station_i, ch);
     int antenna_i = detector->getAntennafromArbAntID( station_i, ch);
-    
+
     if(detector->stations[station_i].strings[string_i].antennas[antenna_i].type!=0) continue; // jump to next channel if this isn't Vpol
-    
+
     TGraph *gr=new TGraph();
-      
+
     int N=stations[station_i].strings[string_i].antennas[antenna_i].V_mimic.size();
-    
+
     for(int i=0;i<N;i++){
-   
+
       gr->SetPoint(i,stations[station_i].strings[string_i].antennas[antenna_i].time_mimic[i], stations[station_i].strings[string_i].antennas[antenna_i].V_mimic[i]);
-    
+
     }// for i
-  
+
     gr->SetNameTitle(Form("WF%dS%02dC%02d", event_num, station_i, ch), Form("Simulated waveform %d, station %d, channel %d;time (ns); voltage (mV)", event_num, station_i, ch));
-    
+
     waveforms.push_back(gr);
-    
+
   }// for ch
-  
+
   return waveforms;
-  
+
 }
 
 vector<TGraph*> Report::getWaveformVectorHpol(Detector *detector, int station_i, int event_num, int run_num){
- 
+
   vector<TGraph*> waveforms;
-  
+
   for(int ch=0;ch<detector->stations[station_i].number_of_antennas; ch++){
-      
+
     int string_i = detector->getStringfromArbAntID( station_i, ch);
     int antenna_i = detector->getAntennafromArbAntID( station_i, ch);
-    
+
     if(detector->stations[station_i].strings[string_i].antennas[antenna_i].type!=1) continue; // jump to next channel if this isn't Hpol
-    
+
     TGraph *gr=new TGraph();
-      
+
     int N=stations[station_i].strings[string_i].antennas[antenna_i].V_mimic.size();
-    
+
     for(int i=0;i<N;i++){
-   
+
       gr->SetPoint(i,stations[station_i].strings[string_i].antennas[antenna_i].time_mimic[i], stations[station_i].strings[string_i].antennas[antenna_i].V_mimic[i]);
-    
+
     }// for i
-  
+
     gr->SetNameTitle(Form("WF%dS%02dC%02d", event_num, station_i, ch), Form("Simulated waveform %d, station %d, channel %d;time (ns); voltage (mV)", event_num, station_i, ch));
-    
+
     waveforms.push_back(gr);
-    
+
   }// for ch
-  
+
   return waveforms;
-  
+
 }
 
 
 vector<double> Report::getHitTimesVector(Detector *detector, int station_i, int polarization){
 
   vector<double> times;
-    
+
   for(int ch=0;ch<detector->stations[station_i].number_of_antennas;ch++){
-    
+
     int string_i = detector->getStringfromArbAntID( station_i, ch);
     int antenna_i = detector->getAntennafromArbAntID( station_i, ch);
-    
+
     if(polarization>=0 && detector->stations[station_i].strings[string_i].antennas[antenna_i].type!=polarization) continue; // jump to next channel if this isn't Hpol/Vpol
 
-    
+
     if(stations[station_i].strings[string_i].antennas[antenna_i].arrival_time.size()){
-   
+
       times.push_back(1e9*stations[station_i].strings[string_i].antennas[antenna_i].arrival_time[0]);// get the direct beam arrival time
-    
+
     }
-  
+
     else times.push_back(-1000); // if there's no ray-trace solution just put something in.
-  
+
   }
-  
+
   return times;
-  
+
 }
 
 vector<double> Report::getHitTimesVectorVpol(Detector *detector, int station_i){
 
   return getHitTimesVector(detector, station_i, 0);
-  
+
 }
 
 vector<double> Report::getHitTimesVectorHpol(Detector *detector, int station_i){
-   
-  return getHitTimesVector(detector, station_i, 1);
-  
-}
 
+  return getHitTimesVector(detector, station_i, 1);
 
+}
diff --git a/Report.h b/Report.h
index 31553e5f..ba8b3801 100644
--- a/Report.h
+++ b/Report.h
@@ -38,336 +38,340 @@ class FFTWComplex;
 using namespace std;
 
 class Surface_antenna_r {
-    public:
+	public:
 
-        ClassDef(Surface_antenna_r,1);
+		ClassDef(Surface_antenna_r,1);
 };
 
 class Antenna_r {
-    public:
+	public:
 
-        // one dimention for number of solutions, (if there,) another dimention for array of information
-        //
+		// one dimention for number of solutions, (if there,) another dimention for array of information
+		//
 
-        int ray_sol_cnt;    // number of RaySolver solutions
+		int ray_sol_cnt;    // number of RaySolver solutions
 
-        //vector <int> trg;    // if antenna recieved any signal or not. 0 : no signal,  1 : yes signal
+		//vector <int> trg;    // if antenna recieved any signal or not. 0 : no signal,  1 : yes signal
 
-        vector <double> view_ang;    //viewing angle
-        vector <double> launch_ang;  //launch angle
-        vector <double> rec_ang;     //receiving angle
-        vector <double> reflect_ang; // surface reflection angle (if 100 : no reflection case)
-        vector <double> Dist;        //Distance between posnu and antenna
-        vector <double> L_att;        //Attenuation factor
-        vector <double> arrival_time;        //time from posnu to antenna (t:0 at posnu)
-        vector <int> reflection;     // non-reflected : 0,  reflected : 1
-        vector <Position> Pol_vector;   // polarization vector at the antenna
-        //vector <Position> n_H;  // normalized vector for H pol
-        //vector <Position> n_V;  // normalized vector for V pol
+		vector <double> view_ang;    //viewing angle
+		vector <double> launch_ang;  //launch angle
+		vector <double> rec_ang;     //receiving angle
+		vector <double> reflect_ang; // surface reflection angle (if 100 : no reflection case)
+		vector <double> Dist;        //Distance between posnu and antenna
+		vector <double> L_att;        //Attenuation factor
+		vector <double> arrival_time;        //time from posnu to antenna (t:0 at posnu)
+		vector <int> reflection;     // non-reflected : 0,  reflected : 1
+		vector <Position> Pol_vector;   // polarization vector at the antenna
+		//vector <Position> n_H;  // normalized vector for H pol
+		//vector <Position> n_V;  // normalized vector for V pol
 
-        // below freq domain simulation output
-        vector < vector <double> > vmmhz;  // signal V/m/MHz for each freq bin
-        //
-        vector < vector <double> > Heff;  // effective height for each freq bin
-        vector <double> Mag;  // magnification factor
-        vector <double> Fresnel;  // Fresnel factor
-        vector <double> Pol_factor;  // Polarization factor
-        
-        vector < vector <double> > Vm_zoom;  // E field before ant T-domain
-        vector < vector <double> > Vm_zoom_T;  // E field before ant T-domain time
-        //vector < vector <double> > Vm_wo_antfactor;  // before applying ApplyAntFactors
-        //vector < vector <double> > VHz_antfactor;  // after applying ApplyAntFactors to vmmhz above ( 1/sqrt2 * 1/dt * 0.5 * heff * pol_factor )
-        //vector < vector <double> > VHz_filter;  // after applying ApplyAntFactors above and then apply filter gain from detector->GetFilterGain
-        //
-        int skip_bins[2]; // for two ray sols
+		// below freq domain simulation output
+		vector < vector <double> > vmmhz;  // signal V/m/MHz for each freq bin
+		//
+		vector < vector <double> > Heff;  // effective height for each freq bin
+		vector <double> Mag;  // magnification factor
+		vector <double> Fresnel;  // Fresnel factor
+		vector <double> Pol_factor;  // Polarization factor
+		
+		vector < vector <double> > Vm_zoom;  // E field before ant T-domain
+		vector < vector <double> > Vm_zoom_T;  // E field before ant T-domain time
+		//vector < vector <double> > Vm_wo_antfactor;  // before applying ApplyAntFactors
+		//vector < vector <double> > VHz_antfactor;  // after applying ApplyAntFactors to vmmhz above ( 1/sqrt2 * 1/dt * 0.5 * heff * pol_factor )
+		//vector < vector <double> > VHz_filter;  // after applying ApplyAntFactors above and then apply filter gain from detector->GetFilterGain
+		//
+		int skip_bins[2]; // for two ray sols
 
-        int Nnew[2]; // new number of bins for V_fotfft array
+		int Nnew[2]; // new number of bins for V_fotfft array
 
-        vector < vector <double> > Vfft;  // signal V preparing for FFT
-        vector < vector <double> > Vfft_noise;  // noise V preparing for FFT
+		vector < vector <double> > Vfft;  // signal V preparing for FFT
+		vector < vector <double> > Vfft_noise;  // noise V preparing for FFT
 
 
-        // below time domain simulation output
-        vector <double> time;   // time of time domain Askaryan radiation
-        vector <double> time_mimic;   // time of time domain Askaryan radiation (same time range with data)
-        vector <double> V_mimic;    // signal + noise waveform which mimics the data (size : NFOUR/2 bin)
+		// below time domain simulation output
+		vector <double> time;   // time of time domain Askaryan radiation
+		vector <double> time_mimic;   // time of time domain Askaryan radiation (same time range with data)
+		vector <double> V_mimic;    // signal + noise waveform which mimics the data (size : NFOUR/2 bin)
 
-        int global_trig_bin; // from V_mimic [0, NFOUR/2] bins, where global trigger occured
+		int global_trig_bin; // from V_mimic [0, NFOUR/2] bins, where global trigger occured
 
-        vector < vector <double> > Ax;     // vector potential x component
-        vector < vector <double> > Ay;
-        vector < vector <double> > Az;
-        vector < vector <double> > V;   // volt signal with all factors applied (as far as we can) (from fft)
+		vector < vector <double> > Ax;     // vector potential x component
+		vector < vector <double> > Ay;
+		vector < vector <double> > Az;
+		vector < vector <double> > V;   // volt signal with all factors applied (as far as we can) (from fft)
 
-        vector <int> SignalExt; // flag if actual signal exist for the ray trace solution
+		vector <int> SignalExt; // flag if actual signal exist for the ray trace solution
 
-        vector <int> SignalBin; // the bin number where the center of signal located. we can compare this value to Trig_Pass value to have likely triggered ray trace solution
+		vector <int> SignalBin; // the bin number where the center of signal located. we can compare this value to Trig_Pass value to have likely triggered ray trace solution
 
 
-        vector <int> noise_ID;      // information about which pure noise waveform is used for trigger analysis
+		vector <int> noise_ID;      // information about which pure noise waveform is used for trigger analysis
 
-        //vector < vector <double> > V_noise; // volt noise signal (with all factors applied as far as we can) (from thermal noise + fft)
+		//vector < vector <double> > V_noise; // volt noise signal (with all factors applied as far as we can) (from thermal noise + fft)
 
-        //vector < vector <double> > V_total; // volt signal + noise with all factors applied as far as we can
+		//vector < vector <double> > V_total; // volt signal + noise with all factors applied as far as we can
 
-        //vector < vector <double> > V_total_diode;   // volt signal + noise with all factors (as far as we can) and convlution with diode (time domain)
+		//vector < vector <double> > V_total_diode;   // volt signal + noise with all factors (as far as we can) and convlution with diode (time domain)
 
-        //vector < vector <double> > V_total_timedelay;   // volt signal + noise with all factors applied and time delay between antennas
-        //
-        //
-        vector <double> PeakV;  // peak voltage in time domain
-        vector <int> Rank;      // rank of peak voltage between antennas (Rank = 0 for 0 signal)
+		//vector < vector <double> > V_total_timedelay;   // volt signal + noise with all factors applied and time delay between antennas
+		//
+		//
+		vector <double> PeakV;  // peak voltage in time domain
+		vector <int> Rank;      // rank of peak voltage between antennas (Rank = 0 for 0 signal)
 
-	//	vector <double> PeakV_fromFullWaveform; // peak voltage in time domain taken from full waveform, including noise at the time of signal insertion
-	//	vector <int> Rank_fromFullWaveform;      // rank of peak voltage between antennas (Rank = 0 for 0 signal)
+		// vector <double> PeakV_fromFullWaveform; // peak voltage in time domain taken from full waveform, including noise at the time of signal insertion
+		// vector <int> Rank_fromFullWaveform;      // rank of peak voltage between antennas (Rank = 0 for 0 signal)
 
-        int Trig_Pass; // 0 if not passed the trigger, 1 if passed the trigger
-        //vector <int> Trig_Pass; // 0 if not passed the trigger, 1 if passed the trigger
+		int Trig_Pass; // 0 if not passed the trigger, 1 if passed the trigger
+		//vector <int> Trig_Pass; // 0 if not passed the trigger, 1 if passed the trigger
 
-        int Likely_Sol; // comparing Trig_Pass and SignalBin value, this value returns which ray trace solution has been triggered (not perfect but most likely)
+		int Likely_Sol; // comparing Trig_Pass and SignalBin value, this value returns which ray trace solution has been triggered (not perfect but most likely)
 
-        int SingleChannelTriggers; // how many bins passed the threshold in this channel (should be equal to size of SCT_threshold_pass).
-        vector <double> SCT_threshold_pass; // for each bin that passed, what was the threshold value at which it passed (for TRIG_SCAN_MODE only). 
+		int SingleChannelTriggers; // how many bins passed the threshold in this channel (should be equal to size of SCT_threshold_pass).
+		vector <double> SCT_threshold_pass; // for each bin that passed, what was the threshold value at which it passed (for TRIG_SCAN_MODE only). 
 	
-	long TotalBinsScannedPerChannel;
+		long TotalBinsScannedPerChannel;
 	
-        vector <int> TooMuch_Tdelay;    // 0 is PeakV is located inside the DATA_BIN_SIZE array,  1 is when PeakV is located outside the DATA_BIN_SIZE so that we can't correctly check if it is triggered or not
+		vector <int> TooMuch_Tdelay;    // 0 is PeakV is located inside the DATA_BIN_SIZE array,  1 is when PeakV is located outside the DATA_BIN_SIZE so that we can't correctly check if it is triggered or not
 
-        
-        void clear ();  // clear all vector format information for next event
-        void clear_useless ( Settings *settings1 );  // clear all vector information which are useless
+		
+		void clear ();  // clear all vector format information for next event
+		void clear_useless ( Settings *settings1 );  // clear all vector information which are useless
 
-        ClassDef(Antenna_r,1);
+		ClassDef(Antenna_r,1);
 };
 
 class String_r {
-    public:
-        //int trg;    // if any antenna trigg in the event. 0 : no antenna in the string trg
-                    //                                    1 : 1 or more antenna trg
+	public:
+		//int trg;    // if any antenna trigg in the event. 0 : no antenna in the string trg
+					//                                    1 : 1 or more antenna trg
 
-        vector <Antenna_r> antennas;
+		vector <Antenna_r> antennas;
 
-        ClassDef(String_r,1);
+		ClassDef(String_r,1);
 };
 
 class Station_r {
-    public:
-        //int trg;    // if any antenna trigg in the event. 0 : no antenna trg
-                    //                                    1: 1 or more antenna trg 
-        vector <String_r> strings;
-        vector <Surface_antenna_r> surfaces;
-
-        double min_arrival_time;    // for each station, minimum arrival time (include all ray_solves). this will be used for time delay between antennas.
-        double max_arrival_time;    // for each station, maximum arrival time (include all ray_solves). this will be used for time delay between antennas.
-        double max_PeakV;           // for each station, maximum PeakV value (include all ray_solves). this will also be used for time delay plot (to set same vertical scale)
-        int Total_ray_sol;          // total number of ray_sols in the stations. If there is 0 Total_ray_sol, we don't need to do trigger check while there is any Total_ray_sol, we do trigger check.
-        int Global_Pass;    // if global trigger passed or not: 0 = not passed, >0 passed, number indicates the first bin in the triggered window of the waveform at which the global trigger passed
-
-        int total_trig_search_bin;  // total number of bins for searching trigger. 
-
-//         int numChan;
-// 	int numChanVpol;
-// 	int numChanHpol;
-        
-        // TDR is for Tunnel Diode Response i.e. the value on which the trigger happened
-        vector <double> TDR_all;
-	vector <double> TDR_all_sorted;
-	vector <double> TDR_Hpol_sorted;
-	vector <double> TDR_Vpol_sorted;
-        
-        ClassDef(Station_r,3);
+	public:
+		//int trg;    // if any antenna trigg in the event. 0 : no antenna trg
+					//                                    1: 1 or more antenna trg 
+		vector <String_r> strings;
+		vector <Surface_antenna_r> surfaces;
+
+		double min_arrival_time;    // for each station, minimum arrival time (include all ray_solves). this will be used for time delay between antennas.
+		double max_arrival_time;    // for each station, maximum arrival time (include all ray_solves). this will be used for time delay between antennas.
+		double max_PeakV;           // for each station, maximum PeakV value (include all ray_solves). this will also be used for time delay plot (to set same vertical scale)
+		int Total_ray_sol;          // total number of ray_sols in the stations. If there is 0 Total_ray_sol, we don't need to do trigger check while there is any Total_ray_sol, we do trigger check.
+		int Global_Pass;    // if global trigger passed or not: 0 = not passed, >0 passed, number indicates the first bin in the triggered window of the waveform at which the global trigger passed
+
+		int total_trig_search_bin;  // total number of bins for searching trigger. 
+
+		//         int numChan;
+		// 	int numChanVpol;
+		// 	int numChanHpol;
+		
+		// TDR is for Tunnel Diode Response i.e. the value on which the trigger happened
+		vector <double> TDR_all;
+		vector <double> TDR_all_sorted;
+		vector <double> TDR_Hpol_sorted;
+		vector <double> TDR_Vpol_sorted;
+		
+		ClassDef(Station_r,3);
 };
 
 
 
 class Report {
-    private:
-        vector <double> noise_phase;    // random noise phase generated in GetNoisePhase()
-
-
-        // variables we need for trigger
-           // test selecting noise waveform
-
-           int noise_pass_nogo; // index for checking if any same noise_ID is used in different chs.
-           int N_noise;     // needed number of noise waveforms (most cases, we will need only 1)
-           int noise_ID[5];    // selected noise waveform ID (we should not need 5 noise waveforms, but just in case)
-           int ch_ID;   // channel ID
-           //double Full_window[detector->params.number_of_strings_station * detector->params.number_of_antennas_string][settings1->DATA_BIN_SIZE];    // entire window for trigger check (diode convlv results for all antennas in a station)
-           //vector < vector <double> > Full_window;  // entire window for trigger check (diode convlv results for all antennas in a station)
-           int max_total_bin;   // to save time, use only necessary number of bins
-           int remain_bin;      // the bin number for not using entire DATA_BIN_SIZE array
-           vector <int> signal_bin;      // the center of bin where signal should locate
-           vector <int> signal_dbin;     // the bin difference between signal bins
-           vector <int> connect_signals;    // if ray_sol time delay is small enough to connect each other
-
-           int triggerCheckLoop(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int scan_mode=1);
-// 	   int triggerCheckLoopScan();
-// 	   int triggerCheckLoopScanNumbers();
+	private:
+		vector <double> noise_phase;    // random noise phase generated in GetNoisePhase()
+
+
+		// variables we need for trigger
+		   // test selecting noise waveform
+
+		   int noise_pass_nogo; // index for checking if any same noise_ID is used in different chs.
+		   int N_noise;     // needed number of noise waveforms (most cases, we will need only 1)
+		   int noise_ID[5];    // selected noise waveform ID (we should not need 5 noise waveforms, but just in case)
+		   int ch_ID;   // channel ID
+		   //double Full_window[detector->params.number_of_strings_station * detector->params.number_of_antennas_string][settings1->DATA_BIN_SIZE];    // entire window for trigger check (diode convlv results for all antennas in a station)
+		   //vector < vector <double> > Full_window;  // entire window for trigger check (diode convlv results for all antennas in a station)
+		   int max_total_bin;   // to save time, use only necessary number of bins
+		   int remain_bin;      // the bin number for not using entire DATA_BIN_SIZE array
+		vector <int> signal_bin;      // the center of bin where signal should locate
+		vector <int> signal_dbin;     // the bin difference between signal bins
+		vector <int> connect_signals;    // if ray_sol time delay is small enough to connect each other
+
+		int triggerCheckLoop(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int scan_mode=1);
+		// int triggerCheckLoopScan();
+		// int triggerCheckLoopScanNumbers();
 	   
-           int saveTriggeredEvent(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int last_trig_bin);
+		int saveTriggeredEvent(Settings *settings1, Detector *detector, Event *event, Trigger *trigger, int stationID, int trig_search_init, int max_total_bin, int trig_window_bin, int last_trig_bin);
 
-           vector < vector < vector <double> > > RayStep;
+		vector < vector < vector <double> > > RayStep;
 
 
-    public:
-           /*
-           double Full_window[16][16384];  // test with array, not vector, diode response
-           double Full_window_V[16][16384];  // test with array, not vector, voltage waveform
-           */
-           vector <int> Passed_chs;
-        //int trg;    // if any antenna in entire detectors trg. 0 : no antenna trg
-                    //                                         1 : 1 or more antenna trg
+	public:
+	   /*
+	   double Full_window[16][16384];  // test with array, not vector, diode response
+	   double Full_window_V[16][16384];  // test with array, not vector, voltage waveform
+	   */
+	   vector <int> Passed_chs;
+		//int trg;    // if any antenna in entire detectors trg. 0 : no antenna trg
+					//                                         1 : 1 or more antenna trg
 
-        Report ();
-        Report (Detector *detector, Settings *settings1);
-        ~Report ();
-    //make the UsefulIcrrStationEvent for use with AraRoot
-    //UsefulIcrrStationEvent theUsefulEvent;
+		Report ();
+		Report (Detector *detector, Settings *settings1);
+		~Report ();
+		//make the UsefulIcrrStationEvent for use with AraRoot
+		//UsefulIcrrStationEvent theUsefulEvent;
 
-    
-        void Initialize (Detector *detector, Settings *settings1);
-
-        //void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger);
-        //void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, UsefulIcrrStationEvent *theUsefulEvent);
+	
+		void Initialize (Detector *detector, Settings *settings1);
 
+		//void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger);
+		//void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, UsefulIcrrStationEvent *theUsefulEvent);
 
-//        void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, UsefulIcrrStationEvent *theUsefulEvent);
-    
-//    void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger);
-    
-    void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, int evt);    
-    
-    
-#ifdef ARA_UTIL_EXISTS
 
-    void MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *trigger, int stationID, int stationIndex, UsefulIcrrStationEvent *theUsefulEvent);
-    void MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *trigger, int stationID, int stationIndex, UsefulAtriStationEvent *theUsefulEvent);
-#endif
-    
-    void ClearUselessfromConnect(Detector *detector, Settings *settings1, Trigger *trigger);
+		// void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, UsefulIcrrStationEvent *theUsefulEvent);
+	
+		// void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger);
+	
+		void Connect_Interaction_Detector (Event *event, Detector *detector, RaySolver *raysolver, Signal *signal, IceModel *icemodel, Settings *settings1, Trigger *trigger, int evt);    
+	
+	
+		#ifdef ARA_UTIL_EXISTS
+			void MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *trigger, int stationID, int stationIndex, UsefulIcrrStationEvent *theUsefulEvent);
+			void MakeUsefulEvent(Detector *detector, Settings *settings1, Trigger *trigger, int stationID, int stationIndex, UsefulAtriStationEvent *theUsefulEvent);
+		#endif
+	
+		void ClearUselessfromConnect(Detector *detector, Settings *settings1, Trigger *trigger);
 
-    
-        void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin, vector <double> &V, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
-        
-        void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin_1, int signalbin_2, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
+	
+		void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin, vector <double> &V, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
+		
+		void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin_1, int signalbin_2, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
 
-        void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin_0, int signalbin_1, int signalbin_2, vector <double> &V0, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
+		void Select_Wave_Convlv_Exchange(Settings *settings1, Trigger *trigger, Detector *detector, int signalbin_0, int signalbin_1, int signalbin_2, vector <double> &V0, vector <double> &V1, vector <double> &V2, int *noise_ID, int ID, int StationIndex);   // literally get noise waveform from trigger class and add signal voltage "V" and do convlv. convlv result will replace the value in Full_window array
 
 
-        void Apply_Gain_Offset(Settings *settings1, Trigger *trigger, Detector *detector, int ID, int StationIndex); // we need to apply a gain offset to the basic waveforms.
+		void Apply_Gain_Offset(Settings *settings1, Trigger *trigger, Detector *detector, int ID, int StationIndex); // we need to apply a gain offset to the basic waveforms.
 
 
 
-        int GetChNumFromArbChID( Detector *detector, int ID, int StationIndex, Settings *settings1);// get actual ch number from arb chID
+		int GetChNumFromArbChID( Detector *detector, int ID, int StationIndex, Settings *settings1);// get actual ch number from arb chID
 
-        Vector GetPolarization (Vector &nnu, Vector &launch_vector);
+		Vector GetPolarization (Vector &nnu, Vector &launch_vector);
 
-        void GetParameters (Position &src, Position &trg, Vector &nnu, double &viewangle, double receive_angle, Vector &launch_vector, Vector &receive_vector, Vector &n_trg_slappy, Vector &n_trg_pokey );    // get viewangle, launch, receive vectors  (it reads launch angle as a viewangle and returns actual viewangle)
+		void GetParameters (Position &src, Position &trg, Vector &nnu, double &viewangle, double receive_angle, Vector &launch_vector, Vector &receive_vector, Vector &n_trg_slappy, Vector &n_trg_pokey );    // get viewangle, launch, receive vectors  (it reads launch angle as a viewangle and returns actual viewangle)
 
-        double GaintoHeight(double gain, double freq, double n_medium);
+		double GaintoHeight(double gain, double freq, double n_medium);
 
-        void ApplyAntFactors(double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vmmhz);
+		void ApplyAntFactors(double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vmmhz);
 
-        void ApplyAntFactors_Tdomain(double AntPhase, double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_real, double &vm_img, Settings *settings1);
+		void ApplyAntFactors_Tdomain(double AntPhase, double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_real, double &vm_img, Settings *settings1);
 
-        void ApplyAntFactors_Tdomain_Transmitter(double AntPhase, double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_real, double &vm_img, Settings *settings1);
+		void ApplyAntFactors_Tdomain_Transmitter(double AntPhase, double heff, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_real, double &vm_img, Settings *settings1);
 
-        void ApplyAntFactors_Tdomain_FirstTwo ( double heff, double heff_lastbin, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_bin0, double &vm_bin1);
+		void ApplyAntFactors_Tdomain_FirstTwo ( double heff, double heff_lastbin, Vector &n_trg_pokey, Vector &n_trg_slappy, Vector &Pol_vector, int ant_type, double &pol_factor, double &vm_bin0, double &vm_bin1);
 
 
-        void ApplyElect_Tdomain(double freq, Detector *detector, double &vm_real, double &vm_img, Settings *settings1);
+		void ApplyElect_Tdomain(double freq, Detector *detector, double &vm_real, double &vm_img, Settings *settings1);
 
-        void ApplyElect_Tdomain_FirstTwo(double freq0, double freq1, Detector *detector, double &vm_bin0, double &vm_bin1);
+		void ApplyElect_Tdomain_FirstTwo(double freq0, double freq1, Detector *detector, double &vm_bin0, double &vm_bin1);
 
 
 
-        void ApplyFilter(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFilter_databin(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFilter_NFOUR(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFilter_OutZero (double freq, Detector *detector, double &vmmhz);
+		void ApplyFilter(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFilter_databin(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFilter_NFOUR(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFilter_OutZero (double freq, Detector *detector, double &vmmhz);
 
 
-        // apply gain in Preamp
-        void ApplyPreamp(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyPreamp_databin(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyPreamp_NFOUR(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyPreamp_OutZero (double freq, Detector *detector, double &vmmhz);
+		// apply gain in Preamp
+		void ApplyPreamp(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyPreamp_databin(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyPreamp_NFOUR(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyPreamp_OutZero (double freq, Detector *detector, double &vmmhz);
 
-	void ApplyNoiseFig_databin(int ch, int bin_n, Detector *detector, double &vmmhz, Settings *settings1);
+		void ApplyNoiseFig_databin(int ch, int bin_n, Detector *detector, double &vmmhz, Settings *settings1);
 
-        // apply gain in FOAM
-        void ApplyFOAM(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFOAM_databin(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFOAM_NFOUR(int bin_n, Detector *detector, double &vmmhz);
-        void ApplyFOAM_OutZero (double freq, Detector *detector, double &vmmhz);
+		// apply gain in FOAM
+		void ApplyFOAM(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFOAM_databin(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFOAM_NFOUR(int bin_n, Detector *detector, double &vmmhz);
+		void ApplyFOAM_OutZero (double freq, Detector *detector, double &vmmhz);
 
 
-        // apply RFCM gain
-        void ApplyRFCM(int ch, int bin_n, Detector *detector, double &vmmhz, double RFCM_OFFSET);
-        void ApplyRFCM_databin(int ch, int bin_n, Detector *detector, double &vmmhz, double RFCM_OFFSET);
+		// apply RFCM gain
+		void ApplyRFCM(int ch, int bin_n, Detector *detector, double &vmmhz, double RFCM_OFFSET);
+		void ApplyRFCM_databin(int ch, int bin_n, Detector *detector, double &vmmhz, double RFCM_OFFSET);
 
 
-        void GetAngleAnt(Vector &rec_vector, Position &antenna, double &ant_theta, double &ant_phi);
+		void GetAngleAnt(Vector &rec_vector, Position &antenna, double &ant_theta, double &ant_phi);
 
-        void GetNoiseWaveforms(Settings *settings1, Detector *detector, double vhz_noise, double *vnoise);
-        void GetNoiseWaveforms_ch(Settings *settings1, Detector *detector, double vhz_noise, double *vnoise, int ch);
+		void GetNoiseWaveforms(Settings *settings1, Detector *detector, double vhz_noise, double *vnoise);
+		void GetNoiseWaveforms_ch(Settings *settings1, Detector *detector, double vhz_noise, double *vnoise, int ch);
 
-        void GetNoisePhase(Settings *settings1);
+		void GetNoisePhase(Settings *settings1);
 
-        void MakeArraysforFFT(Settings *settings1, Detector *detector, int StationIndex, vector <double> &vsignal_array, double *vsignal_forfft);
-        void MakeArraysforFFT(Settings *settings1, Detector *detector, int StationIndex, double *vsignal_array, double *vsignal_forfft);
+		void MakeArraysforFFT(Settings *settings1, Detector *detector, int StationIndex, vector <double> &vsignal_array, double *vsignal_forfft);
+		void MakeArraysforFFT(Settings *settings1, Detector *detector, int StationIndex, double *vsignal_array, double *vsignal_forfft);
 
-        void MakeArraysforFFT_noise(Settings *settings1, Detector *detector,  int StationIndex, vector <double> &vsignal_array, double *vsignal_forfft);
+		void MakeArraysforFFT_noise(Settings *settings1, Detector *detector,  int StationIndex, vector <double> &vsignal_array, double *vsignal_forfft);
 
 
-        double FindPeak (double *waveform, int n);  // same with icemc; trigger->AntTrigger::FindPeak
+		double FindPeak (double *waveform, int n);  // same with icemc; trigger->AntTrigger::FindPeak
 
-        void SetRank(Detector *detector); // set rank (rank of strength of signal at each antenna)
+		void SetRank(Detector *detector); // set rank (rank of strength of signal at each antenna)
 
 
 
-        int GetChannelNum8_LowAnt(int string_num, int antenna_num); // just return ch numbers 1-8 for antenna 0-1 (bottom antennas) and higher ch numbers for antenna 2-3 (top antennas) this is used for only TRIG_ONLY_LOW_CH_ON=1 mode with 
+		int GetChannelNum8_LowAnt(int string_num, int antenna_num); // just return ch numbers 1-8 for antenna 0-1 (bottom antennas) and higher ch numbers for antenna 2-3 (top antennas) this is used for only TRIG_ONLY_LOW_CH_ON=1 mode with 
 
 
-	TGraph *getWaveform(Detector *detector, int ch, int station_i=0, int event_num=0, int run_num=0);
+		TGraph *getWaveform(Detector *detector, int ch, int station_i=0, int event_num=0, int run_num=0);
 
-	vector<TGraph*> getWaveformVector(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
-	vector<TGraph*> getWaveformVectorVpol(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
-	vector<TGraph*> getWaveformVectorHpol(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
+		vector<TGraph*> getWaveformVector(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
+		vector<TGraph*> getWaveformVectorVpol(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
+		vector<TGraph*> getWaveformVectorHpol(Detector *detector, int station_i=0, int event_num=0, int run_num=0);
 	
-	vector<double> getHitTimesVector(Detector *detector, int station_i=0, int polarization=-1);// -1 for all pol, 0 for Vpol, 1: for Hpol
-	vector<double> getHitTimesVectorVpol(Detector *detector, int station_i=0);
-	vector<double> getHitTimesVectorHpol(Detector *detector, int station_i=0);
+		vector<double> getHitTimesVector(Detector *detector, int station_i=0, int polarization=-1);// -1 for all pol, 0 for Vpol, 1: for Hpol
+		vector<double> getHitTimesVectorVpol(Detector *detector, int station_i=0);
+		vector<double> getHitTimesVectorHpol(Detector *detector, int station_i=0);
 
 	
-        vector <double> Vfft_noise_after;   // noise Vfft after get_random_rician
-        vector <double> Vfft_noise_before;   // noise Vfft before get_random_rician
-        //vector <double> V_noise_timedomain;   // noise V timedomain after get_random_rician and inverse fft
-        double Vfft_noise_org;              // V/Hz for thermal noise from Johnson-Nyquist
+		vector <double> Vfft_noise_after;   // noise Vfft after get_random_rician
+		vector <double> Vfft_noise_before;   // noise Vfft before get_random_rician
+		//vector <double> V_noise_timedomain;   // noise V timedomain after get_random_rician and inverse fft
+		double Vfft_noise_org;              // V/Hz for thermal noise from Johnson-Nyquist
+
+		vector <double> V_total_forconvlv; // vector array for pure signal diode convlv result
 
-        vector <double> V_total_forconvlv; // vector array for pure signal diode convlv result
 
+		void clear_useless(Settings *settings1);   // to reduce the size of output AraOut.root, remove some information
 
-        void clear_useless(Settings *settings1);   // to reduce the size of output AraOut.root, remove some information
+		void delete_all(); // delete all informations test
 
-        void delete_all(); // delete all informations test
+		vector <Station_r> stations;
+		vector <String_r> strings;
 
-        vector <Station_r> stations;
-        vector <String_r> strings;
+		double RandomTshift; // for t-domain signal, a factor for random init time shift
 
-        double RandomTshift; // for t-domain signal, a factor for random init time shift
 
+		// test T domain waveform
+		//static const int outbin = 50;
+		static const int outbin = 64;
+		double Tarray[outbin];
+		double Earray[outbin];
 
-        // test T domain waveform
-        //static const int outbin = 50;
-        static const int outbin = 64;
-        double Tarray[outbin];
-        double Earray[outbin];
+		double init_T; // locate zero time at the middle and give random time shift (for interpolated waveforms)
 
-        double init_T; // locate zero time at the middle and give random time shift (for interpolated waveforms)
+		// two parameters for controlling the trigger delay for each channel (only use in real station emulation mode)
+		// and a variable for setting which has the "most" delay
+		double triggerDelay[16];
+		double mostDelay;
 
 
-        ClassDef(Report,1);
+		ClassDef(Report,1);
 
 };
 
diff --git a/Settings.cc b/Settings.cc
index c71fa38e..48e83e01 100644
--- a/Settings.cc
+++ b/Settings.cc
@@ -18,161 +18,156 @@ using namespace std;
 
 Settings::Settings() {
     Initialize();
-//    ReadFile();
-
+    //    ReadFile();
 }
 
 Settings::~Settings() {
-    //default destructor
+        //default destructor
 }
 
 
 void Settings::Initialize() {
 
+    // below : values from icemc Settings class
+        NDISCONES_PASS=3;
 
-// below : values from icemc Settings class
-  NDISCONES_PASS=3;
+        DEBUG=false;                   // debugging option
+        outputdir="outputs"; // directory where outputs go
+        FREQ_LOW_SEAVEYS=200.E6;
+        FREQ_HIGH_SEAVEYS=1200.E6;
+        BW_SEAVEYS=FREQ_HIGH_SEAVEYS-FREQ_LOW_SEAVEYS;
+        SIGMAPARAM=1;  // Connolly et al. 2011 default cross section parametrization
+        SIGMA_FACTOR=1.;   // default sigma factor : 1
+        YPARAM=1;  // 1: Connolly et al. 2011 default y parametrization, 2: Set ELAST_Y yourself
+        ELAST_Y = 0.0;
+        UNBIASED_SELECTION=1.; // (0) pick neutrino interaction in the ice and neutrino from any direction or (1) choose neutrino interaction point in the horizon on the balloon in the ice and neutrino direction on the cerenkov cone
 
-  DEBUG=false;                   // debugging option
-outputdir="outputs"; // directory where outputs go
- FREQ_LOW_SEAVEYS=200.E6;
- FREQ_HIGH_SEAVEYS=1200.E6;
- BW_SEAVEYS=FREQ_HIGH_SEAVEYS-FREQ_LOW_SEAVEYS;
- SIGMAPARAM=1;  // Connolly et al. 2011 default cross section parametrization
- SIGMA_FACTOR=1.;   // default sigma factor : 1
- YPARAM=1;  // 1: Connolly et al. 2011 default y parametrization, 2: Set ELAST_Y yourself
- ELAST_Y = 0.0;
- UNBIASED_SELECTION=1.; // (0) pick neutrino interaction in the ice and neutrino from any direction or (1) choose neutrino interaction point in the horizon on the balloon in the ice and neutrino direction on the cerenkov cone
+        SIGMA_SELECT=0; // when in SIGMAPARAM=1 case, 0 : (default) use mean value, 1 : use upper bound, 2 : use lower bound
+    // end of values from icemc
 
- SIGMA_SELECT=0; // when in SIGMAPARAM=1 case, 0 : (default) use mean value, 1 : use upper bound, 2 : use lower bound
+    ARASIM_VERSION_MAJOR = ARASIM_MAJOR;
+    ARASIM_VERSION_MINOR = ARASIM_MINOR;
+    ARASIM_VERSION_SUBMINOR = ARASIM_SUBMINOR;
+    ARASIM_VERSION = (double)ARASIM_VERSION_MAJOR + (double)ARASIM_VERSION_MINOR * 0.001 + (double)ARASIM_VERSION_SUBMINOR * 0.000001;
 
+    ARAROOT_VERSION = 0.;
 
-// end of values from icemc
+    ARAUTIL_EXISTS = false;
+    #ifdef ARA_UTIL_EXISTS
+        ARAUTIL_EXISTS = true;
+        ARAROOT_VERSION = (double)ARA_ROOT_MAJOR + (double)ARA_ROOT_MINOR * 0.01;
+    #endif
 
- ARASIM_VERSION_MAJOR = ARASIM_MAJOR;
- ARASIM_VERSION_MINOR = ARASIM_MINOR;
- ARASIM_VERSION_SUBMINOR = ARASIM_SUBMINOR;
- ARASIM_VERSION = (double)ARASIM_VERSION_MAJOR + (double)ARASIM_VERSION_MINOR * 0.001 + (double)ARASIM_VERSION_SUBMINOR * 0.000001;
- 
- ARAROOT_VERSION = 0.;
+    NNU=100;
 
- ARAUTIL_EXISTS = false;
-#ifdef ARA_UTIL_EXISTS
- ARAUTIL_EXISTS = true;
- ARAROOT_VERSION = (double)ARA_ROOT_MAJOR + (double)ARA_ROOT_MINOR * 0.01;
-#endif
- 
+    // NEED TO FIGURE OUT A GOOD WAY TO READ THIS IN AND STORE THEM.
+    // INPUT FILE AGAIN?  SOMETHING ELSE?
+    //These were moved here from IceModel under the new compilation scheme
+    ICE_MODEL=0; //Select ice model to be used.  0 = Crust 2.0 , 1 = BEDMAP.
+    NOFZ=1; // 1=depth dependent index of refraction,0=off
+    CONSTANTCRUST=0; // set crust density and thickness to constant values.
+    CONSTANTICETHICKNESS=0; // set ice thickness to constant value
+    FIXEDELEVATION=0; // fix the elevation to the thickness of ice.
+    MOOREBAY=0; //1=use Moore's Bay measured ice field attenuation length for the west land, otherwise use South Pole data
+    USE_ARA_ICEATTENU=1; // use ARA measured ice attenuation value
+
+    EXPONENT=19.; // 10^19 eV neutrinos only
+
+    DETECTOR=1;   //ARA layout with small number of stations
 
-  NNU=100;
+    INTERACTION_MODE=1;   //PickNear mode (0: Aeff mode using sphere surface around station, 1: Veff mode using cylinder volume around station)
 
-  // NEED TO FIGURE OUT A GOOD WAY TO READ THIS IN AND STORE THEM.
-  // INPUT FILE AGAIN?  SOMETHING ELSE?
-  //These were moved here from IceModel under the new compilation scheme
-  ICE_MODEL=0; //Select ice model to be used.  0 = Crust 2.0 , 1 = BEDMAP.
-  NOFZ=1; // 1=depth dependent index of refraction,0=off
-  CONSTANTCRUST=0; // set crust density and thickness to constant values.
-  CONSTANTICETHICKNESS=0; // set ice thickness to constant value
-  FIXEDELEVATION=0; // fix the elevation to the thickness of ice.
-  MOOREBAY=0; //1=use Moore's Bay measured ice field attenuation length for the west land, otherwise use South Pole data
-  USE_ARA_ICEATTENU=1; // use ARA measured ice attenuation value
-  
-  EXPONENT=19.; // 10^19 eV neutrinos only
+    POSNU_RADIUS=3000;    //radius for PickNear method
 
-  DETECTOR=1;   //ARA layout with small number of stations
+    WHICHPARAMETERIZATION=0;  //
 
-  INTERACTION_MODE=1;   //PickNear mode (0: Aeff mode using sphere surface around station, 1: Veff mode using cylinder volume around station)
+    SIMULATION_MODE=1;    // default freq domain simulation
 
-  POSNU_RADIUS=3000;    //radius for PickNear method
+    EVENT_TYPE=0;         // default neutrino only events
 
-  WHICHPARAMETERIZATION=0;  //
+    WAVE_TYPE=0;          // default wave type : plane wave (inside the ice)
 
-  SIMULATION_MODE=1;    // default freq domain simulation
+    LPM=1;                //default : enable LPM effect
 
-  EVENT_TYPE=0;         // default neutrino only events
+    SECONDARIES=1;        //default : enable secondary interactions
 
-  WAVE_TYPE=0;          // default wave type : plane wave (inside the ice)
+    TAUDECAY=1;           //default : let taudecay as secondary interactions
 
-  LPM=1;                //default : enable LPM effect
+    TIMESTEP=(0.625)*1.E-9;  // default, in sec (old default: 0.5E-9, new default 0.625E-9
 
-  SECONDARIES=1;        //default : enable secondary interactions
+    PHASE=90.;            // default : 90 deg phase (it means all imaginary values)
 
-  TAUDECAY=1;           //default : let taudecay as secondary interactions
+    NFOUR=1024;           // default : 1024, same as in icemc
 
-  TIMESTEP=(0.625)*1.E-9;  // default, in sec (old default: 0.5E-9, new default 0.625E-9
+    NOISE=0;              // degault : 0, flat thermal noise, 1 : for TestBed (DETECTOR=3), use Rayleigh distribution fitted for borehole channels
 
-  PHASE=90.;            // default : 90 deg phase (it means all imaginary values)
+    ATMOSPHERE=1;         // default : 1, include atmosphere
 
-  NFOUR=1024;           // default : 1024, same as in icemc
-    
-  NOISE=0;              // degault : 0, flat thermal noise, 1 : for TestBed (DETECTOR=3), use Rayleigh distribution fitted for borehole channels
+    TRIG_SCAN_MODE=0;   // default 0 (old mode) 1: new mode (faster) 2: scan all Pthresh values 3: scan also all N out of 8
 
-  ATMOSPHERE=1;         // default : 1, include atmosphere
+    POWERTHRESHOLD=-6.06; // old default : -6.15, new default: -6.06
 
-  TRIG_SCAN_MODE=0;	// default 0 (old mode) 1: new mode (faster) 2: scan all Pthresh values 3: scan also all N out of 8 
-  
-  POWERTHRESHOLD=-6.06; // old default : -6.15, new default: -6.06
+    MAXT_DIODE=70.E-9;    // default : 70 ns
 
-  MAXT_DIODE=70.E-9;    // default : 70 ns
+    IDELAYBEFOREPEAK_DIODE=(int)(13.E-9 / TIMESTEP);    // default : 13.e-9/TIMESTEP = 33
 
-  IDELAYBEFOREPEAK_DIODE=(int)(13.E-9 / TIMESTEP);    // default : 13.e-9/TIMESTEP = 33
+    IWINDOW_DIODE=(int)(4.E-9 / TIMESTEP);           // default : 4.e-9 / TIMESTEP = 10
 
-  IWINDOW_DIODE=(int)(4.E-9 / TIMESTEP);           // default : 4.e-9 / TIMESTEP = 10
+    DATA_BIN_SIZE=16384;   // default : 16384
 
-  DATA_BIN_SIZE=16384;   // default : 16384
+    NOISE_TEMP=325.;      // default : 325 K
 
-  NOISE_TEMP=325.;      // default : 325 K
+    TRIG_ANALYSIS_MODE=0;    // default : 0, signal + noise
 
-  TRIG_ANALYSIS_MODE=0;    // default : 0, signal + noise
+    TRIG_TIMEOUT=1.E-6;       // default : 1us
 
-  TRIG_TIMEOUT=1.E-6;       // default : 1us
+    TRIG_WINDOW=1.7E-7;       // old default : 110 ns, new default: 170 ns
 
-  TRIG_WINDOW=1.7E-7;       // old default : 110 ns, new default: 170 ns
+    NOISE_EVENTS=16;        // default : 16 events
 
-  NOISE_EVENTS=16;        // default : 16 events
+    DATA_SAVE_MODE=0;         // default : 0 (full mode)
 
-  DATA_SAVE_MODE=0;         // default : 0 (full mode)
+    N_TRIG=3;                 // default : 3 (3 out of all channels in a station)
 
-  N_TRIG=3;                 // default : 3 (3 out of all channels in a station)
+    RANDOM_MODE=1;            // default : 1 (seed is unique in time/space)
 
-  RANDOM_MODE=1;            // default : 1 (seed is unique in time/space)
+    SEED=1; // default: 1, only applies if RANDOM_MODE=0, provides base seed value and run number taken from arguments is added to this value in order to submit multiple repeatable runs instead of only one single long repeatable run
 
-  SEED=1; // default: 1, only applies if RANDOM_MODE=0, provides base seed value and run number taken from arguments is added to this value in order to submit multiple repeatable runs instead of only one single long repeatable run
-    
-  BORE_HOLE_ANTENNA_LAYOUT=0;   // default : 0 (VHVH)
+    BORE_HOLE_ANTENNA_LAYOUT=0;   // default : 0 (VHVH)
 
-  DATA_LIKE_OUTPUT=1; //default : 0 (doesn't write out data-like events)
-    
-  RAYSOL_RANGE=5000; // default : 5000 m
+    DATA_LIKE_OUTPUT=1; //default : 0 (doesn't write out data-like events)
 
-  PICK_POSNU_DEPTH=0;     //default : 0 pick posnu depth from 0 to ice depth
+    RAYSOL_RANGE=5000; // default : 5000 m
 
-  MAX_POSNU_DEPTH=200.;     // default : 200m depth max
+    PICK_POSNU_DEPTH=0;     //default : 0 pick posnu depth from 0 to ice depth
 
-  NNU_THIS_THETA=0;         // default 0: nnu angle pure random, 1: set a specific theta
+    MAX_POSNU_DEPTH=200.;     // default : 200m depth max
 
-  NNU_THETA=0.785;          // default : nnu theta : 45 deg
+    NNU_THIS_THETA=0;         // default 0: nnu angle pure random, 1: set a specific theta
 
-  NNU_D_THETA=0.0873;       // default : nnu d_theta : 5 deg
+    NNU_THETA=0.785;          // default : nnu theta : 45 deg
 
-  NNU_THIS_PHI=0;//default 0: random phi, 1: a specific phi
+    NNU_D_THETA=0.0873;       // default : nnu d_theta : 5 deg
 
-  NNU_PHI=0.785;// default : nnu phi : 45 deg
+    NNU_THIS_PHI=0;//default 0: random phi, 1: a specific phi
+
+    NNU_PHI=0.785;// default : nnu phi : 45 deg
+
+    NNU_D_PHI=0.0873;// default : nnu_d_phi : 5 deg
 
-  NNU_D_PHI=0.0873;// default : nnu_d_phi : 5 deg
 
-    
     CALPULSER_ON=0; // default : calpulsers off
-    
+
     TESTBED_ON=0; // default : 0 stations[0] is ARA1 not Testbed
-    
+
     READGEOM=0; // default : 0 : use idealized geometry and do not read in from sqlite database
-    
+
     V_MIMIC_MODE = 0; // default : 0 - write out all chs where global triggered bin is center of the window
-                        // 1 - same as above 0 mode but apply TestBed ch delay - average BH ch delay
-                        // 2 - same as above 0 mode but apply TestBed ch delay - average BH ch delay + additional delay to match with actual TestBed data waveforms
-    
+                                            // 1 - same as above 0 mode but apply TestBed ch delay - average BH ch delay
+                                            // 2 - same as above 0 mode but apply TestBed ch delay - average BH ch delay + additional delay to match with actual TestBed data waveforms
+
     USE_INSTALLED_TRIGGER_SETTINGS = 0; // default : 0 - use idealized settings for the trigger
-    
+
     NUM_INSTALLED_STATIONS = 4;
 
     CALPUL_OFFCONE_ANGLE = 35.;
@@ -194,7 +189,7 @@ outputdir="outputs"; // directory where outputs go
     CONST_RMSDIODE = 1.346e-13; // also from one run
 
     USE_MANUAL_GAINOFFSET = 0; //if use gain offset file to read values or just use constant gain offset from setup file (default 0 : use file)
-            
+
     MANUAL_GAINOFFSET_VALUE = 1.; // gain offset value
 
     NOISE_WAVEFORM_GENERATE_MODE = 0; // mode 0 (default) will generate noise waveforms newly for each events. other values will use first generated noise waveforms for later events (huge mem usage)
@@ -253,7 +248,7 @@ outputdir="outputs"; // directory where outputs go
 
     ACCUM_TRIG_SEARCH_BINS_STATION0 = 0.; // not actually setting value but gives us how much trigger searched bins there were in the run for station0
 
-    NU_NUBAR_SELECT_MODE = 3; // default : 3 = random nu_nubar based on arXiv:1108.3163, section 3, 0 = just nu, 1 = just nubar 
+    NU_NUBAR_SELECT_MODE = 3; // default : 3 = random nu_nubar based on arXiv:1108.3163, section 3, 0 = just nu, 1 = just nubar
 
 
     SELECT_FLAVOR = 0; // default : 0 = randomly 1:1:1 ratio, 1 : el. 2 : mu, 3 : tau
@@ -269,7 +264,7 @@ outputdir="outputs"; // directory where outputs go
     RAY_TRACE_ICE_MODEL_PARAMS=0; // Default: South Pole values fitted from RICE data
 
     WAVEFORM_LENGTH = 64/2*20; // Default: 64 digitization samples per block / 2 samples per waveform value * 20 blocks (value used for 2013-2016)
-    
+
     WAVEFORM_CENTER = 0; // Default: 0, no offset in waveform centering
 
     POSNU_R = 1000.;
@@ -286,9 +281,8 @@ outputdir="outputs"; // directory where outputs go
 
     CUSTOM_ELECTRONICS=0; //default: 0 -- don't use custom electronics, load regular "ARA_Electronics_TotalGain_TwoFilter.tst"
 
-
     /*
-//arrays for saving read in event features in EVENT_GENERATION_MODE=1
+    //arrays for saving read in event features in EVENT_GENERATION_MODE=1
     EVID[100] = {0};
     NUFLAVORINT[100] = {0};
     NUBAR[100] = {0};
@@ -300,364 +294,393 @@ outputdir="outputs"; // directory where outputs go
     IND_NNU_THETA[100] = {0};
     IND_NNU_PHI[100] = {0};
     */
+
+    DETECTOR_STATION=2; //default: 2, meaning ARA02 (A2)
+    DETECTOR_STATION_LIVETIME_CONFIG=0; //default 0: no special config
+
+    USE_SIGNAL_CHAIN_LOWER_BOUND = 0; // default: 0 -- don't replace signal chain efficiency with lower bound. 1: replace with lower bound
+    SC_EFFICIENCY_ERROR_V = 0.9;     //Lower bound of Vpol signal chain efficiency
+    SC_EFFICIENCY_ERROR_H = 0.68;    //Lower bound of Hpol signal chain efficiency
+    SYSTEMATICS_IceAtten = 0; //Default: Average value (red line) from Eugene's attenuation model (http://radiorm.physics.ohio-state.edu/elog/Write-Ups/170504_105713/Thesis_-_Eugene_Hong.pdf, p. 54), 1 = lower bound, 2 = upper bound
+    SYSTEMATICS_Askaryan = 0; //Default:askaryan signal is not changed at all. =1 scale up the askaryan signal by 12%, =2 scale down the askaryan signal by 12%. The 12% comes from Eugene's thesis, Fg. 5.12.
+    SYSTEMATICS_nofz = 0; // = 0 = default = do nothing; for NOFZ=1 and RAY_TRACE_ICE_MODEL_PARAMS=0, apply the upper bound (=1) and lower bound (=2)
+
 }
 
 void Settings::ReadFile(string setupfile) {
 
-  ifstream setFile (setupfile.c_str());
-  
-  string line, label;
+    ifstream setFile (setupfile.c_str());
 
-  if ( setFile.is_open() ) {
-      while (setFile.good() ) {
-          getline (setFile,line);
+    string line, label;
 
-          if (line[0] != "/"[0]) {
-              label = line.substr(0, line.find_first_of("="));
-              
-              if (label == "NNU") {
-                  NNU = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ICE_MODEL") {
-                  ICE_MODEL = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NOFZ") {
-                  NOFZ = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CONSTANTCRUST") {
-                  CONSTANTCRUST = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CONSTANTICETHICKNESS") {
-                  CONSTANTICETHICKNESS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "FIXEDELEVATION") {
-                  FIXEDELEVATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "MOOREBAY") {
-                  MOOREBAY = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "EXPONENT") {
-                  EXPONENT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DETECTOR") {
-                  DETECTOR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DETECTOR_STATION") {
-                  DETECTOR_STATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "INTERACTION_MODE") {
-                  INTERACTION_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "POSNU_RADIUS") {
-                  POSNU_RADIUS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "WHICHPARAMETERIZATION") {
-                  WHICHPARAMETERIZATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SIMULATION_MODE") {
-                  SIMULATION_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "EVENT_TYPE") {
-                  EVENT_TYPE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "WAVE_TYPE") {
-                  WAVE_TYPE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "LPM") {
-                  LPM = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SECONDARIES") {
-                  SECONDARIES = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TAUDECAY") {
-                  TAUDECAY = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TIMESTEP") {
-                  TIMESTEP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "PHASE") {
-                  PHASE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NFOUR") {
-                  NFOUR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NOISE") {
-                  NOISE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ATMOSPHERE") {
-                  ATMOSPHERE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if(label == "TRIG_SCAN_MODE"){
-                  TRIG_SCAN_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-              else if (label == "POWERTHRESHOLD") {
-                  POWERTHRESHOLD = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DATA_BIN_SIZE") {
-                  DATA_BIN_SIZE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NOISE_TEMP") {
-                  NOISE_TEMP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_ANALYSIS_MODE") {
-                  TRIG_ANALYSIS_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_TIMEOUT") {
-                  TRIG_TIMEOUT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_WINDOW") {
-                  TRIG_WINDOW = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NOISE_EVENTS") {
-                  NOISE_EVENTS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DATA_SAVE_MODE") {
-                  DATA_SAVE_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "N_TRIG") {
-                  N_TRIG = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "RANDOM_MODE") {
-                  RANDOM_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SEED") {
-                  SEED = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "BORE_HOLE_ANTENNA_LAYOUT") {
-                  BORE_HOLE_ANTENNA_LAYOUT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "RAYSOL_RANGE") {
-                  RAYSOL_RANGE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CALPULSER_ON") {
-                  CALPULSER_ON = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TESTBED_ON") {
-                  TESTBED_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "READGEOM") {
-                  cout << "Read in READGEOM" << endl;
-                  READGEOM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "PICK_POSNU_DEPTH") {
-                  PICK_POSNU_DEPTH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "MAX_POSNU_DEPTH") {
-                  MAX_POSNU_DEPTH = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_THIS_THETA") {
-                  NNU_THIS_THETA = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_THETA") {
-                  NNU_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_D_THETA") {
-                  NNU_D_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_THIS_PHI") {
-                  NNU_THIS_PHI = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_PHI") {
-                  NNU_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_D_PHI") {
-                  NNU_D_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
+    if ( setFile.is_open() ) {
+        while (setFile.good() ) {
+            getline (setFile,line);
+            if (line[0] != "/"[0]) {
 
-              else if (label == "DATA_LIKE_OUTPUT") {
-                  DATA_LIKE_OUTPUT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "V_MIMIC_MODE") {
-                  V_MIMIC_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "USE_INSTALLED_TRIGGER_SETTINGS") {
-                  USE_INSTALLED_TRIGGER_SETTINGS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NUM_INSTALLED_STATIONS") {
-                  NUM_INSTALLED_STATIONS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "CALPUL_OFFCONE_ANGLE") {
-                  CALPUL_OFFCONE_ANGLE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CALPUL_AMP") {
-                  CALPUL_AMP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_ONLY_BH_ON") {
-                  TRIG_ONLY_BH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "TRIG_THRES_MODE") {
-                  TRIG_THRES_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "NOISE_CHANNEL_MODE") {
-                  NOISE_CHANNEL_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CONST_MEANDIODE") {
-                  CONST_MEANDIODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "CONST_RMSDIODE") {
-                  CONST_RMSDIODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "USE_TESTBED_RFCM_ON") {
-                  USE_TESTBED_RFCM_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                label = line.substr(0, line.find_first_of("="));
+
+                if (label == "NNU") {
+                    NNU = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ICE_MODEL") {
+                    ICE_MODEL = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOFZ") {
+                    NOFZ = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CONSTANTCRUST") {
+                    CONSTANTCRUST = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CONSTANTICETHICKNESS") {
+                    CONSTANTICETHICKNESS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "FIXEDELEVATION") {
+                    FIXEDELEVATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "MOOREBAY") {
+                    MOOREBAY = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "EXPONENT") {
+                    EXPONENT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DETECTOR") {
+                    DETECTOR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DETECTOR_STATION") {
+                    DETECTOR_STATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DETECTOR_STATION_LIVETIME_CONFIG") {
+                    DETECTOR_STATION_LIVETIME_CONFIG = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "INTERACTION_MODE") {
+                    INTERACTION_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "POSNU_RADIUS") {
+                    POSNU_RADIUS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "WHICHPARAMETERIZATION") {
+                    WHICHPARAMETERIZATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SIMULATION_MODE") {
+                    SIMULATION_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "EVENT_TYPE") {
+                    EVENT_TYPE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "WAVE_TYPE") {
+                    WAVE_TYPE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "LPM") {
+                    LPM = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SECONDARIES") {
+                    SECONDARIES = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TAUDECAY") {
+                    TAUDECAY = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TIMESTEP") {
+                    TIMESTEP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "PHASE") {
+                    PHASE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NFOUR") {
+                    NFOUR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOISE") {
+                    NOISE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ATMOSPHERE") {
+                    ATMOSPHERE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if(label == "TRIG_SCAN_MODE"){
+                    TRIG_SCAN_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "POWERTHRESHOLD") {
+                    POWERTHRESHOLD = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DATA_BIN_SIZE") {
+                    DATA_BIN_SIZE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOISE_TEMP") {
+                    NOISE_TEMP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_ANALYSIS_MODE") {
+                    TRIG_ANALYSIS_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_TIMEOUT") {
+                    TRIG_TIMEOUT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_WINDOW") {
+                    TRIG_WINDOW = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOISE_EVENTS") {
+                    NOISE_EVENTS = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DATA_SAVE_MODE") {
+                    DATA_SAVE_MODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "N_TRIG") {
+                    N_TRIG = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "RANDOM_MODE") {
+                    RANDOM_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SEED") {
+                    SEED = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "BORE_HOLE_ANTENNA_LAYOUT") {
+                    BORE_HOLE_ANTENNA_LAYOUT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "RAYSOL_RANGE") {
+                    RAYSOL_RANGE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CALPULSER_ON") {
+                    CALPULSER_ON = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TESTBED_ON") {
+                    TESTBED_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "READGEOM") {
+                    cout << "Read in READGEOM" << endl;
+                    READGEOM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "PICK_POSNU_DEPTH") {
+                    PICK_POSNU_DEPTH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "MAX_POSNU_DEPTH") {
+                    MAX_POSNU_DEPTH = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_THIS_THETA") {
+                    NNU_THIS_THETA = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_THETA") {
+                    NNU_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_D_THETA") {
+                    NNU_D_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_THIS_PHI") {
+                    NNU_THIS_PHI = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_PHI") {
+                    NNU_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_D_PHI") {
+                    NNU_D_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DATA_LIKE_OUTPUT") {
+                    DATA_LIKE_OUTPUT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "V_MIMIC_MODE") {
+                    V_MIMIC_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "USE_INSTALLED_TRIGGER_SETTINGS") {
+                    USE_INSTALLED_TRIGGER_SETTINGS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NUM_INSTALLED_STATIONS") {
+                    NUM_INSTALLED_STATIONS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CALPUL_OFFCONE_ANGLE") {
+                    CALPUL_OFFCONE_ANGLE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CALPUL_AMP") {
+                    CALPUL_AMP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_ONLY_BH_ON") {
+                    TRIG_ONLY_BH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_THRES_MODE") {
+                    TRIG_THRES_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOISE_CHANNEL_MODE") {
+                    NOISE_CHANNEL_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CONST_MEANDIODE") {
+                    CONST_MEANDIODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "CONST_RMSDIODE") {
+                    CONST_RMSDIODE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "USE_TESTBED_RFCM_ON") {
+                    USE_TESTBED_RFCM_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "RFCM_OFFSET") {
+                    RFCM_OFFSET = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "USE_MANUAL_GAINOFFSET") {
+                    USE_MANUAL_GAINOFFSET = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "MANUAL_GAINOFFSET_VALUE") {
+                    MANUAL_GAINOFFSET_VALUE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NOISE_WAVEFORM_GENERATE_MODE") {
+                    NOISE_WAVEFORM_GENERATE_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "USE_CH_GAINOFFSET") {
+                    USE_CH_GAINOFFSET = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                //else if (label == "GETCHORD_MODE") {
+                        //GETCHORD_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                //}
+                else if (label == "taumodes") {
+                    taumodes = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "BH_ANT_SEP_DIST_ON") {
+                    BH_ANT_SEP_DIST_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_MODE") {
+                    TRIG_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "N_TRIG_V") {
+                    N_TRIG_V = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "N_TRIG_H") {
+                    N_TRIG_H = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "FILL_TREE_MODE") {
+                    FILL_TREE_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ONLY_PASSED_EVENTS") {
+                    ONLY_PASSED_EVENTS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NNU_PASSED") {
+                    NNU_PASSED = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "PICKNEARUNBIASED_R") {
+                    PICKNEARUNBIASED_R = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SHOWER_MODE") {
+                    SHOWER_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SHOWER_STEP") {
+                    SHOWER_STEP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SHOWER_PARAM_MODEL") {
+                    SHOWER_PARAM_MODEL = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ALL_ANT_V_ON") {
+                    ALL_ANT_V_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "PHASE_SKIP_MODE") {
+                    PHASE_SKIP_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DEBUG_MODE_ON") {
+                    DEBUG_MODE_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "DEBUG_SKIP_EVT") {
+                    DEBUG_SKIP_EVT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "V_SATURATION") {
+                    V_SATURATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "OFFCONE_LIMIT") {
+                    OFFCONE_LIMIT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ADDITIONAL_DEPTH_ON") {
+                    ADDITIONAL_DEPTH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ADDITIONAL_DEPTH") {
+                    ADDITIONAL_DEPTH = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "TRIG_ONLY_LOW_CH_ON") {
+                    TRIG_ONLY_LOW_CH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "USE_ARA_ICEATTENU") {
+                    USE_ARA_ICEATTENU = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SIGMA_SELECT") {
+                    SIGMA_SELECT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SIGMAPARAM") {
+                    SIGMAPARAM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SIGMA_FACTOR") {
+                    SIGMA_FACTOR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "YPARAM") {
+                    YPARAM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ELAST_Y") {
+                    ELAST_Y = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "NU_NUBAR_SELECT_MODE") {
+                    NU_NUBAR_SELECT_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SELECT_FLAVOR") {
+                    SELECT_FLAVOR = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "SELECT_CURRENT") {
+                    SELECT_CURRENT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "OUTPUT_TDR_GRAPH") {
+                    OUTPUT_TDR_GRAPH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "AVZ_NORM_FACTOR_MODE") {
+                    AVZ_NORM_FACTOR_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "number_of_stations") {
+                    number_of_stations = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "RAY_TRACE_ICE_MODEL_PARAMS") {
+                    RAY_TRACE_ICE_MODEL_PARAMS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "WAVEFORM_LENGTH") {
+                    WAVEFORM_LENGTH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "WAVEFORM_CENTER") {
+                    WAVEFORM_CENTER = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "POSNU_R") {
+                    POSNU_R = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "POSNU_THETA") {
+                    POSNU_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "POSNU_PHI") {
+                    POSNU_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "ARBITRARY_EVENT_ATTENUATION") {
+                    ARBITRARY_EVENT_ATTENUATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "PICK_ABOVE_HEIGHT") {
+                    PICK_ABOVE_HEIGHT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
+                }
+                else if (label == "EVENT_GENERATION_MODE"){
+                    EVENT_GENERATION_MODE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+                }
+                // else if (label == "EVENT_NUM"){
+                //     EVENT_NUM = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+                // }
+                else if (label == "ANTENNA_MODE"){
+                    ANTENNA_MODE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+                }
+                else if (label == "APPLY_NOISE_FIGURE"){
+                    APPLY_NOISE_FIGURE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+                }
+                else if (label == "CUSTOM_ELECTRONICS"){
+                    CUSTOM_ELECTRONICS = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+                }
+              else if (label == "USE_SIGNAL_CHAIN_LOWER_BOUND"){
+                  USE_SIGNAL_CHAIN_LOWER_BOUND = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+              }
+              else if (label == "SC_EFFICIENCY_ERROR_V"){
+                  SC_EFFICIENCY_ERROR_V = atof(line.substr(line.find_first_of("=") + 1).c_str());
+              }
+              else if (label == "SC_EFFICIENCY_ERROR_H"){
+              	   SC_EFFICIENCY_ERROR_H = atof(line.substr(line.find_first_of("=") + 1).c_str());
+              }
+              else if (label == "SYSTEMATICS_IceAtten"){
+              	   SYSTEMATICS_IceAtten = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+              }
+              else if (label == "SYSTEMATICS_Askaryan"){
+                   SYSTEMATICS_Askaryan = atoi(line.substr(line.find_first_of("=") + 1).c_str());
+              }
+              else if (label == "SYSTEMATICS_nofz"){
+                   SYSTEMATICS_nofz = atoi(line.substr(line.find_first_of("=") + 1).c_str());
               }
-              else if (label == "RFCM_OFFSET") {
-                  RFCM_OFFSET = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "USE_MANUAL_GAINOFFSET") {
-                  USE_MANUAL_GAINOFFSET = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "MANUAL_GAINOFFSET_VALUE") {
-                  MANUAL_GAINOFFSET_VALUE = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NOISE_WAVEFORM_GENERATE_MODE") {
-                  NOISE_WAVEFORM_GENERATE_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "USE_CH_GAINOFFSET") {
-                  USE_CH_GAINOFFSET = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              //else if (label == "GETCHORD_MODE") {
-                  //GETCHORD_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              //}
-              else if (label == "taumodes") {
-                  taumodes = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "BH_ANT_SEP_DIST_ON") {
-                  BH_ANT_SEP_DIST_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_MODE") {
-                  TRIG_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "N_TRIG_V") {
-                  N_TRIG_V = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "N_TRIG_H") {
-                  N_TRIG_H = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "FILL_TREE_MODE") {
-                  FILL_TREE_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ONLY_PASSED_EVENTS") {
-                  ONLY_PASSED_EVENTS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NNU_PASSED") {
-                  NNU_PASSED = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "PICKNEARUNBIASED_R") {
-                  PICKNEARUNBIASED_R = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SHOWER_MODE") {
-                  SHOWER_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SHOWER_STEP") {
-                  SHOWER_STEP = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SHOWER_PARAM_MODEL") {
-                  SHOWER_PARAM_MODEL = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ALL_ANT_V_ON") {
-                  ALL_ANT_V_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "PHASE_SKIP_MODE") {
-                  PHASE_SKIP_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DEBUG_MODE_ON") {
-                  DEBUG_MODE_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "DEBUG_SKIP_EVT") {
-                  DEBUG_SKIP_EVT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "V_SATURATION") {
-                  V_SATURATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "OFFCONE_LIMIT") {
-                  OFFCONE_LIMIT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ADDITIONAL_DEPTH_ON") {
-                  ADDITIONAL_DEPTH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "ADDITIONAL_DEPTH") {
-                  ADDITIONAL_DEPTH = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "TRIG_ONLY_LOW_CH_ON") {
-                  TRIG_ONLY_LOW_CH_ON = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "USE_ARA_ICEATTENU") {
-                  USE_ARA_ICEATTENU = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SIGMA_SELECT") {
-                  SIGMA_SELECT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "SIGMAPARAM") {
-                  SIGMAPARAM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "SIGMA_FACTOR") {
-                  SIGMA_FACTOR = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "YPARAM") {
-                  YPARAM = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "ELAST_Y") {
-                 ELAST_Y = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "NU_NUBAR_SELECT_MODE") {
-                  NU_NUBAR_SELECT_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-              else if (label == "SELECT_FLAVOR") {
-                  SELECT_FLAVOR = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "SELECT_CURRENT") {
-                  SELECT_CURRENT = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }
-              else if (label == "OUTPUT_TDR_GRAPH") {
-                  OUTPUT_TDR_GRAPH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }       
-              else if (label == "AVZ_NORM_FACTOR_MODE") {
-                  AVZ_NORM_FACTOR_MODE = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-              }              
-	      else if (label == "number_of_stations") {
-		number_of_stations = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "RAY_TRACE_ICE_MODEL_PARAMS") {
-		RAY_TRACE_ICE_MODEL_PARAMS = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "WAVEFORM_LENGTH") {
-		WAVEFORM_LENGTH = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "WAVEFORM_CENTER") {
-		WAVEFORM_CENTER = atoi( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "POSNU_R") {
-		POSNU_R = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "POSNU_THETA") {
-		POSNU_THETA = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "POSNU_PHI") {
-		POSNU_PHI = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "ARBITRARY_EVENT_ATTENUATION") {
-		ARBITRARY_EVENT_ATTENUATION = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-	      else if (label == "PICK_ABOVE_HEIGHT") {
-		PICK_ABOVE_HEIGHT = atof( line.substr(line.find_first_of("=") + 1).c_str() );
-	      }
-              else if (label == "EVENT_GENERATION_MODE"){
-                  EVENT_GENERATION_MODE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
-              }
-	      //              else if (label == "EVENT_NUM"){
-	      //                  EVENT_NUM = atoi(line.substr(line.find_first_of("=") + 1).c_str());
-	      //              }
-              else if (label == "ANTENNA_MODE"){
-                  ANTENNA_MODE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
-              }
-              else if (label == "APPLY_NOISE_FIGURE"){
-                  APPLY_NOISE_FIGURE = atoi(line.substr(line.find_first_of("=") + 1).c_str());
-              }
-              else if (label == "CUSTOM_ELECTRONICS"){
-              	   CUSTOM_ELECTRONICS = atoi(line.substr(line.find_first_of("=") + 1).c_str());
-              }
-
-
 
 
           }
@@ -683,7 +706,9 @@ void Settings::ReadEvtFile(string evtfile){
                 double d, f, g, h, i, j, k;
                 if (!(iss >> a >> b >> c >> d >> e >> f >> g >> h >> i >> j >> k))
                     break;
-/*                EVID[i] = atoi(a.c_str());
+
+                /*
+                EVID[i] = atoi(a.c_str());
                 NUFLAVORINT[i] = atoi(b.c_str());
                 NUBAR[i] = atoi(c.c_str());
                 PNU[i] = atof(d.c_str());
@@ -693,8 +718,8 @@ void Settings::ReadEvtFile(string evtfile){
                 Z[i] = atof(h.c_str());
                 THETA[i] = atof(i.c_str());
                 PHI[i] = atof(j.c_str());
-*/
-/*
+                */
+                /*
                 EVID[l] = a;
                 NUFLAVORINT[l] = b;
                 NUBAR[l] = c;
@@ -705,7 +730,7 @@ void Settings::ReadEvtFile(string evtfile){
                 IND_POSNU_PHI[l] = h;
                 IND_NNU_THETA[l] = i;
                 IND_NNU_PHI[l] = j;
-*/
+                */
                 EVID.push_back(a);
                 NUFLAVORINT.push_back(b);
                 NUBAR.push_back(c);
@@ -723,11 +748,10 @@ void Settings::ReadEvtFile(string evtfile){
             }
         }
         evtFile.close();
-	if (NNU == 0 || NNU > EVID.size()){
-	  //	  EVENT_NUM = EVID.size();
-	  NNU = EVID.size();
-	}
-	
+        if (NNU == 0 || NNU > EVID.size()){
+            // EVENT_NUM = EVID.size();
+            NNU = EVID.size();
+        }
     }
     else
         cout << "Unable to open " << evtfile << " file!" << endl;
@@ -778,8 +802,8 @@ int Settings::CheckCompatibilitiesDetector(Detector *detector) {
 
     // check if there's enough system temperature values prepared for NOISE_CHANNEL_MODE=1
     if (NOISE_CHANNEL_MODE==1) {// use different system temperature values for different chs
-      if (DETECTOR==3 && (detector->params.number_of_antennas > (int)(detector->Temp_TB_ch.size())) ) {
-	  cout << detector->params.number_of_antennas << " : " <<(int)(detector->Temp_TB_ch.size()) << endl;
+        if (DETECTOR==3 && (detector->params.number_of_antennas > (int)(detector->Temp_TB_ch.size())) ) {
+            cout << detector->params.number_of_antennas << " : " <<(int)(detector->Temp_TB_ch.size()) << endl;
             cerr<<"System temperature values are not enough for all channels! Check number of channels you are using and numbers in data/system_temperature.csv"<<endl;
             num_err++;
         }
@@ -796,33 +820,31 @@ int Settings::CheckCompatibilitiesSettings() {
     /*
     // if INTERACTION_MODE is 0 (sphere area and obtain Aeff), make sure using GETCHORD_MODE=1
     if (INTERACTION_MODE==0) { // picknear_sphere mode
-        if (GETCHORD_MODE==0) { // but use old getchord mode (not working!)
-            cerr<<"In INTERACTION_MODE=0, you have to use GETCHORD_MODE=1"<<endl; 
-            num_err++;
-        }
+            if (GETCHORD_MODE==0) { // but use old getchord mode (not working!)
+                    cerr<<"In INTERACTION_MODE=0, you have to use GETCHORD_MODE=1"<<endl;
+                    num_err++;
+            }
     }
     else if (INTERACTION_MODE==1) { // picknear_cylinder mode
-        if (GETCHORD_MODE==1) { // but use new getchord mode (not working!)
-            cerr<<"In INTERACTION_MODE=1, you have to use GETCHORD_MODE=0"<<endl; 
-            num_err++;
-        }
+            if (GETCHORD_MODE==1) { // but use new getchord mode (not working!)
+                    cerr<<"In INTERACTION_MODE=1, you have to use GETCHORD_MODE=0"<<endl;
+                    num_err++;
+            }
     }
     */
 
     // if BH_ANT_SEP_DIST_ON=1, we can't use READGEOM=1 (actual installed geom)
     if (BH_ANT_SEP_DIST_ON==1 && READGEOM==1) {
-        cerr<<"BH_ANT_SEP_DIST_ON=1 is only available in ideal station geom (READGEOM=0)!"<<endl; 
+        cerr<<"BH_ANT_SEP_DIST_ON=1 is only available in ideal station geom (READGEOM=0)!"<<endl;
         num_err++;
     }
 
     // TRIG_MODE=1 (Vpol, Hpol separated) will not work with testbed station mode
     if (TRIG_MODE==1 && DETECTOR==3) {
-        cerr<<"TRIG_MODE=1 is not available in TestBed mode (DETECTOR=3)!"<<endl; 
+        cerr<<"TRIG_MODE=1 is not available in TestBed mode (DETECTOR=3)!"<<endl;
         num_err++;
     }
 
-
-
     // check modes which will only work for actual installed TestBed case
     //
     if (TRIG_ONLY_BH_ON==1 && DETECTOR!=3) {
@@ -833,9 +855,9 @@ int Settings::CheckCompatibilitiesSettings() {
     /*
     //if (NOISE_CHANNEL_MODE==1 && DETECTOR!=3) {
     if (NOISE_CHANNEL_MODE==1 && DETECTOR!=3 && TRIG_ONLY_LOW_CH_ON!=1) {
-        //cerr<<"NOISE_CHANNEL_MODE=1 only works with DETECTOR=3!"<<endl;
-        cerr<<"NOISE_CHANNEL_MODE=1 only works with DETECTOR=3 or TRIG_ONLY_LOW_CH_ON=1"<<endl;
-        num_err++;
+            //cerr<<"NOISE_CHANNEL_MODE=1 only works with DETECTOR=3!"<<endl;
+            cerr<<"NOISE_CHANNEL_MODE=1 only works with DETECTOR=3 or TRIG_ONLY_LOW_CH_ON=1"<<endl;
+            num_err++;
     }
     */
 
@@ -887,7 +909,7 @@ int Settings::CheckCompatibilitiesSettings() {
         cerr<<"V_MIMIC_MODE=1 and 2 only works with DETECTOR=3!"<<endl;
         num_err++;
     }
-    
+
     if (USE_MANUAL_GAINOFFSET==1 && USE_CH_GAINOFFSET==1) {
         cerr<<"Can not use USE_MANUAL_GAINOFFSET=1 and USE_CH_GAINOFFSET=1 same time!"<<endl;
         num_err++;
@@ -929,41 +951,81 @@ int Settings::CheckCompatibilitiesSettings() {
     }
     /*
     if(NOISE == 2 && (DETECTOR==0 || DETECTOR==1 || DETECTOR==2)){
-      cerr << "CALIBRATION_MODE=1 doesn't work with DETECTOR=0,1,2" << endl;
-      cerr << "CALIBRATION_MODE controls the response from installed stations 2,3 and thus has no real relevance for DETECTOR=0,1,2" << endl;
-      num_err++;
+        cerr << "CALIBRATION_MODE=1 doesn't work with DETECTOR=0,1,2" << endl;
+        cerr << "CALIBRATION_MODE controls the response from installed stations 2,3 and thus has no real relevance for DETECTOR=0,1,2" << endl;
+        num_err++;
     }
     */
-
+    if (SYSTEMATICS_IceAtten > 0 && (USE_ARA_ICEATTENU==0)) {
+        cerr<<"SYSTEMATICS_IceAtten=1,2 doesn't work with USE_ARA_ICEATTENU=0"<<endl;
+        cerr<<"SYSTEMATICS_IceAtten=1,2 are upper/lower bounds for Eugene's attenuation model, which doesn't correspond to USE_ARA_ICEATTENU=0 "<<endl;
+        num_err++;
+    }
     // This is for installed stations
     if (DETECTOR == 4 ) {
-      if (ARAUTIL_EXISTS == false){
-	cerr << "DETECTOR=4 only works with an installation of AraRoot" << endl;
-	num_err++;
-      } else {
-	
-	cerr << "DETECTOR is set to 4" << endl; 
-	cerr << "Setting READGEOM to 1" << endl;
-	READGEOM=1;
-
-	cerr << "Setting number_of_stations to 1" << endl;
-	number_of_stations = 1;
-
-	if (DETECTOR_STATION <0 || DETECTOR_STATION >= NUM_INSTALLED_STATIONS){
-	  cerr << "DETECTOR_STATION is not set to a valid station number" << endl;
-	  num_err++;
-	}
-		
-      }
+        if (ARAUTIL_EXISTS == false){
+            cerr << "DETECTOR=4 only works with an installation of AraRoot" << endl;
+            num_err++;
+        } else {
+
+            cerr << "DETECTOR is set to 4" << endl;
+            cerr << "Setting READGEOM to 1" << endl;
+            READGEOM=1;
+
+            cerr << "Setting number_of_stations to 1" << endl;
+            number_of_stations = 1;
+
+            if (DETECTOR_STATION <0 || DETECTOR_STATION >= NUM_INSTALLED_STATIONS){
+                cerr << "DETECTOR_STATION is not set to a valid station number" << endl;
+                num_err++;
+            }
+            if(DETECTOR_STATION_LIVETIME_CONFIG>0){
+                if((int)DETECTOR_STATION==2 || (int)DETECTOR_STATION==3){
+                    cerr<<"DETECTOR_STATION_LIVETIME_CONFIG is set to "<<DETECTOR_STATION_LIVETIME_CONFIG<<endl;
+                    if(DETECTOR_STATION_LIVETIME_CONFIG>5){
+                        cerr<<" DETECTOR_STATION_LIVETIME_CONFIG is set to "<<DETECTOR_STATION_LIVETIME_CONFIG<<" but there are only five expected configurations"<<endl;
+                        num_err++;
+                    }
+                }
+                else{
+                    cerr<<" DETECTOR_STATION_LIVETIME_CONFIG is set to "<<DETECTOR_STATION_LIVETIME_CONFIG<<" but DETECTOR_STATION is "<<DETECTOR_STATION<<endl;
+                    cerr<<" DETECTOR_STATION_LIVETIME_CONFIG is only valid for A2 and A3 "<<endl;
+                    num_err++;
+                }
+            }
+        }
     }
 
-   //Check that DETECTOR_STATION=0 is only used with DETECTOR=3
-   if (DETECTOR_STATION==0 && DETECTOR!=3){
-      cerr << " DETECTOR_STATION=0 doesn't work with DETECTOR!=3. If you want to work with TestBed, use DETECTOR=3 & DETECTOR_STATION=0" << endl;
-      num_err++;
-   }
 
+    //Check that DETECTOR_STATION=0 is only used with DETECTOR=3
+    if (DETECTOR_STATION==0 && DETECTOR!=3){
+       cerr << " DETECTOR_STATION=0 doesn't work with DETECTOR!=3. If you want to work with TestBed, use DETECTOR=3 & DETECTOR_STATION=0" << endl;
+       num_err++;
+    }
 
-    return num_err;
+    //Signal chain uncertainty estimate is only compatible with using different TV/BV
+    if (ANTENNA_MODE != 1 && USE_SIGNAL_CHAIN_LOWER_BOUND > 0){
+       cerr<<"USE_SIGNAL_CHAIN_LOWER_BOUND>0 doesn't work with ANTENNA_MODE!=1"<<endl;
+       num_err++;
+    }
 
+    //Signal chain uncertainty estimate is only compatible with simulating with actual installed stations
+    if (DETECTOR != 4 && USE_SIGNAL_CHAIN_LOWER_BOUND > 0){
+       cerr<<"USE_SIGNAL_CHAIN_LOWER_BOUND>0 doesn't work with DETECTOR!=4."<<endl;
+       num_err++;
+    }
+
+    //Signal chain uncertainty estimate is only compatible with simulating with actual installed stations 1 and above. TestBed is a different beast
+    if (DETECTOR == 4 && DETECTOR_STATION==0 && USE_SIGNAL_CHAIN_LOWER_BOUND > 0){
+       cerr<<"USE_SIGNAL_CHAIN_LOWER_BOUND>0 doesn't work with DETECTOR_STATION==0. The signal chain measurements are done with ARA deep stations."<<endl;
+       num_err++;
+    }
+
+    if(SYSTEMATICS_nofz>0 && RAY_TRACE_ICE_MODEL_PARAMS!=0){
+        cerr<<"SYSTEMATICS_nofz>0 only works with the default AraSim model RAY_TRACE_ICE_MODEL_PARAMS=0."<<endl;
+        num_err++;
+    }
+
+
+    return num_err;
 }
diff --git a/Settings.h b/Settings.h
index 34205ff3..e47bdd5a 100644
--- a/Settings.h
+++ b/Settings.h
@@ -10,7 +10,7 @@ class Detector;
 using namespace std;
 //using std::string;
 
-class Settings 
+class Settings
 {
     protected:
 
@@ -25,18 +25,18 @@ class Settings
         int CheckCompatibilitiesSettings();// check if settings are not compatible to each other
         int CheckCompatibilitiesDetector(Detector *detector);// check if settings are not compatible to each other. checking against initialized Detector *detector object
 
-	int ARASIM_VERSION_MAJOR;
+        int ARASIM_VERSION_MAJOR;
         int ARASIM_VERSION_MINOR;
         int ARASIM_VERSION_SUBMINOR;
         double ARASIM_VERSION;
 
         double ARAROOT_VERSION;
-	bool ARAUTIL_EXISTS;
+        bool ARAUTIL_EXISTS;
         int NNU;
 
-  // NEED TO FIGURE OUT A GOOD WAY TO READ THIS IN AND STORE THEM.
-  // INPUT FILE AGAIN?  SOMETHING ELSE?
-  //These were moved here from IceModel under the new compilation scheme
+        // NEED TO FIGURE OUT A GOOD WAY TO READ THIS IN AND STORE THEM.
+        // INPUT FILE AGAIN?  SOMETHING ELSE?
+        //These were moved here from IceModel under the new compilation scheme
         int ICE_MODEL; //Select ice model to be used.  0 = Crust 2.0 , 1 = BEDMAP.
         int NOFZ; // 1=depth dependent index of refraction,0=off
         int CONSTANTCRUST; // set crust density and thickness to constant values.
@@ -49,10 +49,14 @@ class Settings
 
         int DETECTOR;   // choose detector layout
 
-	int DETECTOR_STATION; // for DETECTOR=4, indicates the single station to be simulated
-	                      // 0 = testbed, 1 = A1, 2 = A2, 3 = A3
+        int DETECTOR_STATION; // for DETECTOR=4, indicates the single station to be simulated
+                           //default is 2
+                          // 0 = testbed, 1 = A1, 2 = A2, 3 = A3
 
-	int number_of_stations; // the number of stations to be used in the simulation
+        int DETECTOR_STATION_LIVETIME_CONFIG; // only to be used with DETECTOR=4 (real station), and DETECTOR_STATION=2 or =3 (A2/A3)
+                                                // default is 0, which means do nothing special based on configurations
+
+        int number_of_stations; // the number of stations to be used in the simulation
 
         int INTERACTION_MODE;   // method to choose interaction point posnu. 0 : PickUnbiased, 1 : PickNear, 2 : PickExact, 3 : PickAboveIce
 
@@ -83,7 +87,7 @@ class Settings
         int ATMOSPHERE;         // include atmosphere 1, no 0
 
         int TRIG_SCAN_MODE;
-        
+
         double POWERTHRESHOLD;  // power threshold value. default -4.41 (same with icemc powerthreshold)
 
         double MAXT_DIODE;      // diode model max time, default : 70.e-9s
@@ -108,13 +112,13 @@ class Settings
         int N_TRIG;         // number of coincidence channels triggered in TRIG_WINDOW default : 3
 
         int RANDOM_MODE;    // 0 : same random number generate, 1 : TRandom3(0) used. purely randomly generated (seed is guaranteed to be unique in space and time)
-    
+
         int SEED; // default: 1, only applies if RANDOM_MODE=0, provides base seed value and run number taken from arguments is added to this value in order to submit multiple repeatable runs instead of only one single long repeatable run
 
         int BORE_HOLE_ANTENNA_LAYOUT;   // 0 = (V-H-V-H), 1 = (V-H-V), 2 = (V-H-V-V), 3 = (V-H-H-H), 4 = (V-H-H) default : 0
-    
+
         int DATA_LIKE_OUTPUT; // Formerly WRITE_ALL_EVENTS, the mode numbering has changed as well
-	                      // 0 - don't write any information to the data-like output tree
+                          // 0 - don't write any information to the data-like output tree
                               // 1 - only write globally triggered events,
                               // 2 - Write all event events including events that are not globally triggered
         // Note: NNU is the number of neutrinos that have been thrown in total, not just globally triggered events
@@ -123,20 +127,20 @@ class Settings
         double RAYSOL_RANGE;    // direct distance limit to do raysolver. If distance between posnu and antenna is bigger than RAYSOL_RANGE, AraSim will not try RaySol for that event. Default : 3000 m
 
         int CALPULSER_ON; // 0: no calpulsers in event list, 1: only throws calpulser 1 events, 2: only throws calpulser 2 events, 3: throws both calpulser 1 and 2 events alternating between them, 4: throws calpulser 1 and 2 events integrated with the simulated data (not yet implemented)
-    
+
         int TESTBED_ON;
-    
+
         int READGEOM;
-    
+
         int V_MIMIC_MODE; // default : 0 - write out all chs where global triggered bin is center of the window
                         // 1 - same as above 0 mode but apply TestBed ch delay - average BH ch delay
                         // 2 - same as above 0 mode but apply TestBed ch delay - average BH ch delay + additional delay to match with actual TestBed data waveforms
-    
+
         int USE_INSTALLED_TRIGGER_SETTINGS; // default : 0 - use idealized settings for the trigger
         //other options:  1 - use trigger settings for installed stations, i.e. trigger window, etc.
-    
+
         int NUM_INSTALLED_STATIONS; // the number of stations including the testbed that are in reality installed in the ice and have position and electronics information
-    
+
         int PICK_POSNU_DEPTH;  // whether use MAX_POSNU_DEPTH or not. 0 : pick posnu depth full ice depth, 1 : pick posnu depth only MAX_POSNU_DEPTH
 
         double MAX_POSNU_DEPTH;  // maximum posnu depth when above PICK_POSNU_DEPTH=1
@@ -164,17 +168,17 @@ class Settings
         int NOISE_CHANNEL_MODE;    // if using same noise temp for all chs (0, default), using diff temp for all chs (1), using diff temp for first 8 chs and share same temp for other chs (2), using same noise temp but allowing to use noise
 
         double CONST_MEANDIODE;
-    
+
         double CONST_RMSDIODE;  // in case NOISE_CHANNEL_MODE = 1, just using this CONST_RMSDIODE value for threshold
 
 
         int USE_TESTBED_RFCM_ON;    // use RFCM measurement for testbed or not (default 0)
-    
+
         double RFCM_OFFSET;  // if above USE_TESTBED_RFCM_ON = 1, we need RFCM attenuator factor cancel (default 80)
 
 
         int USE_MANUAL_GAINOFFSET; //whether use additional gain offset after all ant, elect chain. default 0 : don't apply any additional gain, 1 :  use gain offset
-    
+
         int USE_CH_GAINOFFSET; // only if USE_MANUAL_GAINOFFSET = 1, default 0 : apply constant gain to all channels which is MANUAL_GAINOFFSET_VALUE, 1 : apply ch gain offset by using data/preamp_gain_offset.csv file (only installed TestBed mode available)
 
 
@@ -194,13 +198,13 @@ class Settings
         int TRIG_MODE; // default 0 : if any antennas got passed N_TRIG or more, global trig. 1 : either Vpol or Hpol antennas got passed N_TRIG_V or N_TRIG_H respectively, global trig.
 
         int N_TRIG_V; // default : 3 (3 out of Vpolchannels in a station)
-    
+
         int N_TRIG_H; // default : 3 (3 out of Hpol channels in a station)
 
         int FILL_TREE_MODE; // default 0 : fill tree for all events, 1 : fill tree only usable posnu events, 2 : fill tree only trigger passed events
 
-	int ONLY_PASSED_EVENTS; // 0: NNU represents the number of neutrinos total thrown in the simulation, 1: NNU represents the number of globally triggered neutrinos desired in the output file in the end
-	int NNU_PASSED; // Number of neutrinos allowed to pass the trigger - for ONLY_PASSE_EVENTS, loop until this is reached, otherwise just a storage value
+        int ONLY_PASSED_EVENTS; // 0: NNU represents the number of neutrinos total thrown in the simulation, 1: NNU represents the number of globally triggered neutrinos desired in the output file in the end
+        int NNU_PASSED; // Number of neutrinos allowed to pass the trigger - for ONLY_PASSE_EVENTS, loop until this is reached, otherwise just a storage value
 
         double PICKNEARUNBIASED_R; // radius of the sphere surrounding the detector for INTERACTION_MODE=3, current default value is 5000 m
 
@@ -211,12 +215,12 @@ class Settings
 
         int SHOWER_PARAM_MODEL; // shower profile parameter, 0 = fit function from Jaime, 1 = fit from Carl (OSU), default 0
 
-        double OFFCONE_LIMIT; // offcone cut angel (deg) to reduce computation time 
+        double OFFCONE_LIMIT; // offcone cut angel (deg) to reduce computation time
 
 
         int ALL_ANT_V_ON; // default 1 : use both Vpol, Hpol ant gain from Vpol ant model but for Hpol ant case response is in Hpol, not Vpol, 0 : use Vpol ant gain from Vpol model, Hpol ant gain from Hpol model (where Hpol ant model is not reliable).
 
-    
+
         int PHASE_SKIP_MODE; // skip applying phase in t-domain mode (SIMULATION_MODE = 1). default 0 : don't skip (apply all phase), 1 : only upto Askaryan radiation, 2 : only upto antenna
 
 
@@ -228,24 +232,24 @@ class Settings
         double V_SATURATION; // default 1., output voltage saturation due to amplifier limit. by default it's +-1. V
 
 
-    
+
         int ADDITIONAL_DEPTH_ON; // whether add more depth to each antenas, default : 0 (not on)
-    
+
         double ADDITIONAL_DEPTH; // additional depth value, default 100, only applied when ADDITIONAL_DEPTH_ON=1
 
 
-        
+
         int TRIG_ONLY_LOW_CH_ON;    // if trigger will occur with all chs (0, default) or only lower 8 chs (1)
 
-    
+
         double ACCUM_TRIG_SEARCH_BINS_STATION0; // not actually setting value but gives us how much trigger searched bins there were in the run
 
 
-	int OUTPUT_TDR_GRAPH;// saves a few example graphs of the tunnel diode response for a triggered event
-	
-	
-    
-        int NU_NUBAR_SELECT_MODE; // default : 3 = random nu_nubar based on arXiv:1108.3163, section 3, 0 = just nu, 1 = just nubar 
+        int OUTPUT_TDR_GRAPH;// saves a few example graphs of the tunnel diode response for a triggered event
+
+
+
+        int NU_NUBAR_SELECT_MODE; // default : 3 = random nu_nubar based on arXiv:1108.3163, section 3, 0 = just nu, 1 = just nubar
 
 
         int SELECT_FLAVOR; // default : 0 = random 1:1:1, 1: e, 2: mu, 3: tau
@@ -255,42 +259,42 @@ class Settings
 
         int AVZ_NORM_FACTOR_MODE; // default : 1 : don't apply sqrt(2) (actually applied but cancel that) as realft assume Hn as double-sided spectrum (invFFT normalization factor 2/N) and also remove dF binning factor in MakeArraysforFFT function, 0 : use normalization factors like in old version
 
-	int RAY_TRACE_ICE_MODEL_PARAMS; // which parameter set is used for the exponential ice model (defined in RayTrace_IceModel.cc) 
-	//0 : default, South Pole model (fitted from RICE data
-	//1 : South Pole model fitted from RICE #2
-	//2 : South Pole (Eisen (2003))
-	//3 : South Pole (Gow)
-	//10 : Moore's Bay Model 1
-	//11 : Moore's Bay Model 2
-	//20 : Byrd (Ebimuna (1983))
-	//30 : Mizuho (Ebimuna (1983))
+        int RAY_TRACE_ICE_MODEL_PARAMS; // which parameter set is used for the exponential ice model (defined in RayTrace_IceModel.cc)
+        //0 : default, South Pole model (fitted from RICE data
+        //1 : South Pole model fitted from RICE #2
+        //2 : South Pole (Eisen (2003))
+        //3 : South Pole (Gow)
+        //10 : Moore's Bay Model 1
+        //11 : Moore's Bay Model 2
+        //20 : Byrd (Ebimuna (1983))
+        //30 : Mizuho (Ebimuna (1983))
 
-	int WAVEFORM_LENGTH; // the number of samples in the waveform length for V_mimic and UsefulAtriStationEvent, default: 64/2*20 = 640
+        int WAVEFORM_LENGTH; // the number of samples in the waveform length for V_mimic and UsefulAtriStationEvent, default: 64/2*20 = 640
 
-	int WAVEFORM_CENTER; // the relative location of the center of the write-out window with respect to the last triggered bin (which is laced at the center of the window by default), this effectively provides a global delay in the write-out window across all channels: positive values shift the write-out window to later times in the waveform, negative values shift the window to earlier times, default: 0
+        int WAVEFORM_CENTER; // the relative location of the center of the write-out window with respect to the last triggered bin (which is laced at the center of the window by default), this effectively provides a global delay in the write-out window across all channels: positive values shift the write-out window to later times in the waveform, negative values shift the window to earlier times, default: 0
 
-	double POSNU_R; // default: 1000; meters from station center
-	double POSNU_THETA; // default: -PI/4; elevation angle from station center coordinates
-	double POSNU_PHI; // default: 0; azimuth angle from station center coordinates
-	// Only using INTERACTION_MODE = 2, these values set the position of the interaction point; can be used in EVENT_TYPE = 0 and 10
+        double POSNU_R; // default: 1000; meters from station center
+        double POSNU_THETA; // default: -PI/4; elevation angle from station center coordinates
+        double POSNU_PHI; // default: 0; azimuth angle from station center coordinates
+        // Only using INTERACTION_MODE = 2, these values set the position of the interaction point; can be used in EVENT_TYPE = 0 and 10
 
-	double ARBITRARY_EVENT_ATTENUATION; // attenuation of the waveform intensity for arbitrary event waveforms
-	double PICK_ABOVE_HEIGHT;
+        double ARBITRARY_EVENT_ATTENUATION; // attenuation of the waveform intensity for arbitrary event waveforms
+        double PICK_ABOVE_HEIGHT;
 
         int EVENT_GENERATION_MODE;//default: 0: not event mode, 1: event mode
-	//        int EVENT_NUM;//number of events to read in, using EVENT_GENERATION_MODE=1, default initial 0: read in the number of events in the input file, resets to total number of events read in
+        //        int EVENT_NUM;//number of events to read in, using EVENT_GENERATION_MODE=1, default initial 0: read in the number of events in the input file, resets to total number of events read in
 
-	int ANTENNA_MODE; // 0: old default antenna models bicone/rotated dipole
-	                   // 1: using different antenna response for the top Vpol antennas, otherwise same as old default
+        int ANTENNA_MODE; // 0: old default antenna models bicone/rotated dipole
+                       // 1: using different antenna response for the top Vpol antennas, otherwise same as old default
 
-	int APPLY_NOISE_FIGURE; // 0: do not apply new noise figure from Thomas Meures 2016
-	                        // 1: apply new noise figure to data
+        int APPLY_NOISE_FIGURE; // 0: do not apply new noise figure from Thomas Meures 2016
+                            // 1: apply new noise figure to data
 
-	int CUSTOM_ELECTRONICS; //0 (default): use the regular "ARA_Electronics_TotalGain_TwoFilter.txt" file
-							//1 : load a custom electronics file, stored as "custom_electronics.txt" in the `data` directory
+        int CUSTOM_ELECTRONICS; //0 (default): use the regular "ARA_Electronics_TotalGain_TwoFilter.txt" file
+                            //1 : load a custom electronics file, stored as "custom_electronics.txt" in the `data` directory
 
 
-//arrays for saving read in event features in EVENT_GENERATION_MODE=1
+        //arrays for saving read in event features in EVENT_GENERATION_MODE=1
         vector<int> EVID;
         vector<int> NUFLAVORINT;
         vector<int> NUBAR;
@@ -305,125 +309,130 @@ class Settings
 
 
 
-    // below : values from icemc
-    
-    
-    int UNBIASED_SELECTION;
-    int WHICH; // which payload to use 0=Anita-lite,1=Ross,2=Smex,3=make your own
-    int CYLINDRICALSYMMETRY; // is it cylindrically symmetric =1 if which=1,2, =0 if which=0
-    // if which=3 then 0 or 1
-    double SIGMA_FACTOR; // factor to multiply cross section by for error analysis
-    int SIGMAPARAM; // 0=Reno, 1=Connolly et al. 2011 for cross section parametrization
-    int YPARAM; // 0=Reno, 1=Connolly et al. 2011 for cross section parametrization, 2 = a specific elast_y
-    double ELAST_Y;
+        // below : values from icemc
+
+            int UNBIASED_SELECTION;
+            int WHICH; // which payload to use 0=Anita-lite,1=Ross,2=Smex,3=make your own
+            int CYLINDRICALSYMMETRY; // is it cylindrically symmetric =1 if which=1,2, =0 if which=0
+            // if which=3 then 0 or 1
+            double SIGMA_FACTOR; // factor to multiply cross section by for error analysis
+            int SIGMAPARAM; // 0=Reno, 1=Connolly et al. 2011 for cross section parametrization
+            int YPARAM; // 0=Reno, 1=Connolly et al. 2011 for cross section parametrization, 2 = a specific elast_y
+            double ELAST_Y;
 
-    int SIGMA_SELECT; // when in SIGMAPARAM=1 case, 0 : (default) use mean value, 1 : use upper bound, 2 : use lower bound
+            int SIGMA_SELECT; // when in SIGMAPARAM=1 case, 0 : (default) use mean value, 1 : use upper bound, 2 : use lower bound
 
-    int SIGNAL_FLUCT;  // 1=add noise fluctuation to signal or 0=do not
-    int TRIGGERSCHEME;  // frequency domain voltage, frequency domain energy, time domain diode integration
-    int ZEROSIGNAL;  // zero the signal to see how many of our hits are noise hits
-    int REMOVEPOLARIZATION; //Disable polarizations
-    
-    int EVENTSMAP;//whether draw the events distribution map
-    
-    int WHICHRAYS;  // how many rays to look at (1) direct only (2) direct and down-going.
+            int SIGNAL_FLUCT;  // 1=add noise fluctuation to signal or 0=do not
+            int TRIGGERSCHEME;  // frequency domain voltage, frequency domain energy, time domain diode integration
+            int ZEROSIGNAL;  // zero the signal to see how many of our hits are noise hits
+            int REMOVEPOLARIZATION; //Disable polarizations
 
-// trigger
-int LCPRCP; // 1 for circular polarization trigger, 0 for V and H
-int JUSTVPOL; // 0 for both polarizations, 1 for just V polarization
-// doesn't allow for both LCPRCP=1 and JUSTVPOL=1
-//int FIFTHBAND; // 1 to include 0.2-1.2 GHz as a frequency band if JUSTVPOL==1
-//int NFOLD=3;  // how many channels must pass the trigger - in old mechanism - only used for anita-lite
-int NFOLD;  // how many channels must pass the trigger - in old mechanism - only used for anita-lite
+            int EVENTSMAP;//whether draw the events distribution map
 
+            int WHICHRAYS;  // how many rays to look at (1) direct only (2) direct and down-going.
 
-//int CHMASKING=1; // whether or not to include channel masking
-//int PHIMASKING=1; // whether or not to include phi masking  
-int CHMASKING; // whether or not to include channel masking
-int PHIMASKING; // whether or not to include phi masking  
+            // trigger
+            int LCPRCP; // 1 for circular polarization trigger, 0 for V and H
+            int JUSTVPOL; // 0 for both polarizations, 1 for just V polarization
+            // doesn't allow for both LCPRCP=1 and JUSTVPOL=1
+            //int FIFTHBAND; // 1 to include 0.2-1.2 GHz as a frequency band if JUSTVPOL==1
+            //int NFOLD=3;  // how many channels must pass the trigger - in old mechanism - only used for anita-lite
+            int NFOLD;  // how many channels must pass the trigger - in old mechanism - only used for anita-lite
 
-//int NLAYERS=0;
-//int NANTENNAS=0;
 
-int NLAYERS;
-int NANTENNAS;
+            //int CHMASKING=1; // whether or not to include channel masking
+            //int PHIMASKING=1; // whether or not to include phi masking
+            int CHMASKING; // whether or not to include channel masking
+            int PHIMASKING; // whether or not to include phi masking
 
-/* int ONLYFINAL=1; // only write to final histogram */
-/* int HIST_MAX_ENTRIES=10000; //maximum number of events to put in histograms */
-/* int HIST=1;          //write to histograms  */
+            //int NLAYERS=0;
+            //int NANTENNAS=0;
 
-int ONLYFINAL; // only write to final histogram
-int HIST_MAX_ENTRIES; //maximum number of events to put in histograms
-int HIST;          //write to histograms 
-double BW; // BANDWIDTH
-//int DISCONES=1; // whether or not to use discones
-int DISCONES; // whether or not to use discones
+            int NLAYERS;
+            int NANTENNAS;
 
-//double NDISCONES_PASS=3; // number of discones needed to pass
-double NDISCONES_PASS; // number of discones needed to pass
+            /* int ONLYFINAL=1; // only write to final histogram */
+            /* int HIST_MAX_ENTRIES=10000; //maximum number of events to put in histograms */
+            /* int HIST=1;          //write to histograms  */
 
-int BORESIGHTS; // whether to loop over boresights
-int SLAC; // whether or not we are simulating the slac run
-double SLACSLOPE; // slope of the ice
-double SLACICELENGTH;  // length of the block of ice
-double SLAC_HORIZDIST; // horizontal distance from interaction to center of payload at slac beam test
-double SLAC_DEPTH; // vertical depth of interaction at slac beam test
-double SLAC_HORIZ_DEPTH; // horizontal depth of interaction at slac
+            int ONLYFINAL; // only write to final histogram
+            int HIST_MAX_ENTRIES; //maximum number of events to put in histograms
+            int HIST;          //write to histograms
+            double BW; // BANDWIDTH
+            //int DISCONES=1; // whether or not to use discones
+            int DISCONES; // whether or not to use discones
 
-int ROUGHNESS; // include effects of surface roughness
-int FIRN; // whether or not to include the firn
+            //double NDISCONES_PASS=3; // number of discones needed to pass
+            double NDISCONES_PASS; // number of discones needed to pass
 
-//int SLOPEY=1; // 1=slopeyness on, 0=slopeyness off
-//double SLOPEYSIZE=0.012; // This determines size of the slopeyness (0.10=5.4, 0.20=7.4 deg mean)
+            int BORESIGHTS; // whether to loop over boresights
+            int SLAC; // whether or not we are simulating the slac run
+            double SLACSLOPE; // slope of the ice
+            double SLACICELENGTH;  // length of the block of ice
+            double SLAC_HORIZDIST; // horizontal distance from interaction to center of payload at slac beam test
+            double SLAC_DEPTH; // vertical depth of interaction at slac beam test
+            double SLAC_HORIZ_DEPTH; // horizontal depth of interaction at slac
 
-int SLOPEY; // 1=slopeyness on, 0=slopeyness off
-double SLOPEYSIZE; // This determines size of the slopeyness (0.10=5.4, 0.20=7.4 deg mean)
+            int ROUGHNESS; // include effects of surface roughness
+            int FIRN; // whether or not to include the firn
 
- bool DEBUG;
-string outputdir; // directory where outputs go
+            //int SLOPEY=1; // 1=slopeyness on, 0=slopeyness off
+            //double SLOPEYSIZE=0.012; // This determines size of the slopeyness (0.10=5.4, 0.20=7.4 deg mean)
 
-//double THERMALNOISE_FACTOR=1.0; // factor to multiply thermal noise for error analysis
-double THERMALNOISE_FACTOR; // factor to multiply thermal noise for error analysis
+            int SLOPEY; // 1=slopeyness on, 0=slopeyness off
+            double SLOPEYSIZE; // This determines size of the slopeyness (0.10=5.4, 0.20=7.4 deg mean)
 
-//double FREQ_LOW_SEAVEYS=200.E6; // min frequency for seaveys
-//const double FREQ_HIGH_SEAVEYS=1200.E6; // max frequency for seaveys
+             bool DEBUG;
+            string outputdir; // directory where outputs go
 
-double FREQ_LOW_SEAVEYS; // min frequency for seaveys
-double FREQ_HIGH_SEAVEYS; // max frequency for seaveys
- double BW_SEAVEYS;
- //int FORSECKEL=1; // Make array of strength of signal across frequencies for different viewing angles.
-int FORSECKEL; // Make array of strength of signal across frequencies for different viewing angles.
+            //double THERMALNOISE_FACTOR=1.0; // factor to multiply thermal noise for error analysis
+            double THERMALNOISE_FACTOR; // factor to multiply thermal noise for error analysis
 
-double ROUGHSIZE; // roughness size
+            //double FREQ_LOW_SEAVEYS=200.E6; // min frequency for seaveys
+            //const double FREQ_HIGH_SEAVEYS=1200.E6; // max frequency for seaveys
 
+            double FREQ_LOW_SEAVEYS; // min frequency for seaveys
+            double FREQ_HIGH_SEAVEYS; // max frequency for seaveys
+             double BW_SEAVEYS;
+             //int FORSECKEL=1; // Make array of strength of signal across frequencies for different viewing angles.
+            int FORSECKEL; // Make array of strength of signal across frequencies for different viewing angles.
 
-/* int ICE_MODEL=0; //Select ice model to be used.  0 = Crust 2.0 , 1 = BEDMAP. */
-/* int NOFZ=1; // 1=depth dependent index of refraction,0=off */
-/* int CONSTANTCRUST=0; // set crust density and thickness to constant values. */
-/* int CONSTANTICETHICKNESS=0; // set ice thickness to constant value */
-/* int FIXEDELEVATION=0; // fix the elevation to the thickness of ice. */
-/* int MOOREBAY=0; //1=use Moore's Bay measured ice field attenuation length for the west land, otherwise use South Pole data */
-/* int USEPOSITIONWEIGHTS=1;// whether or not to restrict the neutrino position so it is within the horizon of the balloon */
-/* int WRITE_FILE=0; //Select whether or not to write a new input file for CreateHorizons */
+            double ROUGHSIZE; // roughness size
 
-int USEPOSITIONWEIGHTS;// whether or not to restrict the neutrino position so it is within the horizon of the balloon
-int WRITE_FILE; //Select whether or not to write a new input file for CreateHorizons
 
-int MINRAY;
-int MAXRAY;
+            /* int ICE_MODEL=0; //Select ice model to be used.  0 = Crust 2.0 , 1 = BEDMAP. */
+            /* int NOFZ=1; // 1=depth dependent index of refraction,0=off */
+            /* int CONSTANTCRUST=0; // set crust density and thickness to constant values. */
+            /* int CONSTANTICETHICKNESS=0; // set ice thickness to constant value */
+            /* int FIXEDELEVATION=0; // fix the elevation to the thickness of ice. */
+            /* int MOOREBAY=0; //1=use Moore's Bay measured ice field attenuation length for the west land, otherwise use South Pole data */
+            /* int USEPOSITIONWEIGHTS=1;// whether or not to restrict the neutrino position so it is within the horizon of the balloon */
+            /* int WRITE_FILE=0; //Select whether or not to write a new input file for CreateHorizons */
 
-int horizontal_banana_points;
-  int vertical_banana_points;
 
+            int USEPOSITIONWEIGHTS;// whether or not to restrict the neutrino position so it is within the horizon of the balloon
+            int WRITE_FILE; //Select whether or not to write a new input file for CreateHorizons
 
+            int MINRAY;
+            int MAXRAY;
 
+            //Implemented for signal chain calibration uncertainty estimate - 12/17/2019 MYL
+            int USE_SIGNAL_CHAIN_LOWER_BOUND; //Switch to replace the signal chain efficiency by its error lower bound. Use this for systematic estimation. Default 0: do not use lower bound. 1: use lower bound.
+            double SC_EFFICIENCY_ERROR_V; //Total estimated signal chain efficiency error for Vpol from Meures. Measured in power. Only used when USE_SIGNAL_CHAIN_LOWER_BOUND=1. Default: 0.9, representing a 10% deficiency
+            double SC_EFFICIENCY_ERROR_H; //Total estimated signal chain efficiency error for Hpol from Meures. Measured in power. Only used when USE_SIGNAL_CHAIN_LOWER_BOUND=1. Default: 0.68, representing a 32% deficiency
 
- // end of values from icemc
 
+            int horizontal_banana_points;
+            int vertical_banana_points;
+            int SYSTEMATICS_IceAtten; //Default: Average value (red line) from Eugene's attenuation model (http://radiorm.physics.ohio-state.edu/elog/Write-Ups/170504_105713/Thesis_-_Eugene_Hong.pdf, p. 54), 1 = lower bound, 2 = upper bound
+            int SYSTEMATICS_Askaryan; //Default:askaryan signal is not changed at all. =1 scale up the askaryan signal by 12%, =2 scale down the askaryan signal by 12%. The 12% comes from Eugene's thesis, Fg. 5.12.
+            int SYSTEMATICS_nofz; // = 0 = default = do nothing; for NOFZ=1 and RAY_TRACE_ICE_MODEL_PARAMS=0, apply the upper bound (=1) and lower bound (=2)
 
-  ClassDef(Settings,1);
+        // end of values from icemc
+
+
+ ClassDef(Settings,1);
 
 
 };
 #endif
-
diff --git a/Spectra.cc b/Spectra.cc
index 4c75763c..a6c8acf4 100644
--- a/Spectra.cc
+++ b/Spectra.cc
@@ -33,7 +33,7 @@ Spectra::Spectra(double EXPONENT) {
 
   double Emuons[E_bin]; // E dN/dE/dA/dt for neutrinos that are produced as muon neutrinos or muon antineutrinos.
   double Eelectrons[E_bin];// E dN/dE/dA/dt for neutrinos that are produced as electron neutrinos or muon antineutrinos.
-  
+
   for (int i=0;i<E_bin;i++) {
     energy[i]=16.+((double)i)*0.12; // initial E_bin = 50. energy = 16 ~ 22 eV
     Emuons[i]=-30.;
@@ -87,13 +87,13 @@ Spectra::Spectra(double EXPONENT) {
   {
       pnu_EXPONENT = EXPONENT;
   }
-  
+
   else if (EXPONENT_model>=510. && EXPONENT_model<=650.) // g.n. added so we can have simulations at E^2=17.8 not just whole numbers
   {
       pnu_EXPONENT = (EXPONENT_model - 400)/10;
 	cout<<"**************** energy is "<<pnu_EXPONENT<<" *******************"<<endl;
   }
-  
+
   else if (EXPONENT==30.) // ESS baseline model. Used to be EXPONENT "0"
   {
       E_bin = 9;
@@ -112,7 +112,7 @@ Spectra::Spectra(double EXPONENT) {
     Eelectrons[9]=-30.; // 20.5 punt------ not using above here
     Eelectrons[10]=-30.; // 21.0 punt
     Eelectrons[11]=-30.; // 21.5 punt
-  
+
     // lower curve of Figure 9 of ES&S
     // astro-ph/0101216
        Emuons[0]=-17.1;  //16.
@@ -127,7 +127,7 @@ Spectra::Spectra(double EXPONENT) {
        Emuons[9]=-19.9; // 20.5 punt------not using above here
        Emuons[10]=-30.; // 21.0 punt
        Emuons[11]=-30.; // 21.5 punt
-  
+
     for (int i=0;i<E_bin;i++) {
         energy[i] = 16.+((double)i)/2.;   // in log, in eV
         EdNdEdAdt[i] = log10( pow(10., Eelectrons[i]) + pow(10., Emuons[i]) );   // in log
@@ -155,7 +155,7 @@ Spectra::Spectra(double EXPONENT) {
     Eelectrons[9]=-30.; // 20.5 punt------ not using above here
     Eelectrons[10]=-30.; // 21.0 punt
     Eelectrons[11]=-30.; // 21.5 punt
-    
+
     // muon component of Figure 4 of ES&S
     // astro-ph/0101216
     Emuons[0]=-17.8; // 16.
@@ -170,10 +170,10 @@ Spectra::Spectra(double EXPONENT) {
     Emuons[9]=-30.; // 20.5 punt
     Emuons[10]=-30.; // 21.0 punt
     Emuons[11]=-30.; // 21.5 punt
-    
+
     for(int i=0;i<E_bin;i++)
       emuratio[i]=Eelectrons[i]/Emuons[i];
-    
+
     // upper curve in Figure 9 of ES&S
     // astro-ph/0101216
     Emuons[0]=-16.85;  //16.
@@ -188,20 +188,20 @@ Spectra::Spectra(double EXPONENT) {
     Emuons[9]=-19.75; // 20.5 punt
     Emuons[10]=-30.; // 21.0 punt
     Emuons[11]=-30.; // 21.5 punt
-    
-    
+
+
     for(int i=0;i<E_bin;i++) {
       Eelectrons[i]=Emuons[i]*emuratio[i];
       cout << "Eelectrons, Emuons are " << Eelectrons[i] << " " << Emuons[i] << "\n";
     }
-  
+
     for (int i=0;i<E_bin;i++) {
       energy[i] = 16.+((double)i)/2.;   // in log, in eV
       EdNdEdAdt[i]=log10( pow(10.,Eelectrons[i]) + pow(10.,Emuons[i]) );  // in log.
       E2dNdEdAdt[i] = EdNdEdAdt[i] + (energy[i] - 9.);    // in log, in GeV
       cout << "EdNdEdAdt are " << EdNdEdAdt[i] << "\n";
     }
-    
+
   } // end if ESS-cosmological constant
 
 
@@ -268,7 +268,7 @@ Spectra::Spectra(double EXPONENT) {
   {
       GetFlux("Ave2005_Fe_Emax21.5.dat");
   }
-  
+
   else if (EXPONENT==202.)
   {
       GetFlux("Ave2005_Fe_Emax22.0.dat");
@@ -314,6 +314,13 @@ Spectra::Spectra(double EXPONENT) {
       GetFlux("Kotera2010_max.dat");
   }
 
+  else if (EXPONENT==225.)
+  {
+      GetFlux("Cuoco_CenA.dat");
+      cout << "\033[1;31mUsing Cuoco et al. flux\033[0m\n";
+
+  }
+
 
 
 
@@ -331,9 +338,9 @@ Spectra::Spectra(double EXPONENT) {
     for (int i=0;i<12;i++) {
       E2dNdEdAdt[i]=log10(EdNdEdAdt[i])+energy[i]-9.;
     }
-    
+
     spectrum=new TSpline5("spectrum",energy,EdNdEdAdt,12);
-    
+
   }
   else
     // find the max so we can normalise it
@@ -341,9 +348,9 @@ Spectra::Spectra(double EXPONENT) {
 */
 
 
-  // From log to linear!!  
+  // From log to linear!!
   for (int i=0;i<E_bin;i++) {
-      EdNdEdAdt[i] = pow(10, EdNdEdAdt[i]);     //to linear 
+      EdNdEdAdt[i] = pow(10, EdNdEdAdt[i]);     //to linear
       E2dNdEdAdt[i] = pow(10, E2dNdEdAdt[i]);   //to linear
 //      E2dNdEdAdt[i]=log10(EdNdEdAdt[i])+energy[i]-9.;
 
@@ -353,19 +360,19 @@ Spectra::Spectra(double EXPONENT) {
 //--------------------------------------------------
 //   gEdNdEdAdt = new TGraph(E_bin, energy, EdNdEdAdt);
 //   gE2dNdEdAdt = new TGraph(E_bin, energy, E2dNdEdAdt);
-// 
+//
 //   sEdNdEdAdt = new TSpline3("sEdNdEdAdt", gEdNdEdAdt);
 //   sE2dNdEdAdt = new TSpline3("sE2dNdEdAdt", gE2dNdEdAdt);
-//-------------------------------------------------- 
+//--------------------------------------------------
 
   maxflux=Tools::dMax(EdNdEdAdt,E_bin);
 
 
- 
+
 }
 
 double  Spectra::GetNuEnergy_bin() {
-  
+
   double thisenergy=16.; // arbitrary initialisation
   double thisflux=2.; // initialise higher than max
   double max=1.;
@@ -374,19 +381,19 @@ double  Spectra::GetNuEnergy_bin() {
   double minenergy=Tools::dMin(energy,E_bin);
   // this uses the dartboard approach
   //cout << "minenergy, maxenergy are " << minenergy << " " << maxenergy << "\n";
-  
+
   if (EXPONENT_model>=10. && EXPONENT_model<30.) {
       return pow(10.,pnu_EXPONENT);
   }
 
   else {
-  
+
   while(thisflux>max) {
-    // pick an energy  
+    // pick an energy
     thisenergy=Rand3.Rndm()*(maxenergy-minenergy)+minenergy; // pick energy at random between the highest and lowest
-    // the energy array is actually filled with energy exponents 
+    // the energy array is actually filled with energy exponents
     // and thisenergy starts from 0 so it has an offset
-    
+
     energybin=Tools::Getifreq(thisenergy,minenergy,maxenergy,E_bin);
     //max=gspectrum[(int)EXPONENT]->Eval(thisenergy,0,"S")/maxflux; // this is the maximum the normalized flux can be in this bin, always less than 1
     max=EdNdEdAdt[energybin]/maxflux;
@@ -394,7 +401,7 @@ double  Spectra::GetNuEnergy_bin() {
   } //while
   return pow(10.,thisenergy);
   }
-	
+
 } //Pick Neutrino Energy
 
 
@@ -402,7 +409,7 @@ double  Spectra::GetNuEnergy_bin() {
 
 
 double  Spectra::GetNuEnergy() {
-  
+
   double thisenergy=16.; // arbitrary initialisation
   double thisflux=2.; // initialise higher than max
   double max=1.;
@@ -411,19 +418,19 @@ double  Spectra::GetNuEnergy() {
   double minenergy=Tools::dMin(energy,E_bin);
   // this uses the dartboard approach
   //cout << "minenergy, maxenergy are " << minenergy << " " << maxenergy << "\n";
-  
+
   if ((EXPONENT_model>=10. && EXPONENT_model<30.) || (EXPONENT_model>=510. && EXPONENT_model<=650.)) {
       return pow(10.,pnu_EXPONENT);
   }
 
   else {
-  
+
   while(thisflux>max) {
-    // pick an energy  
+    // pick an energy
     thisenergy=Rand3.Rndm()*(maxenergy-minenergy)+minenergy; // pick energy at random between the highest and lowest
-    // the energy array is actually filled with energy exponents 
+    // the energy array is actually filled with energy exponents
     // and thisenergy starts from 0 so it has an offset
-    
+
     // get interpolated flux at "thisenergy"
     max=SimpleLinearInterpolation_value(E_bin, energy, EdNdEdAdt, thisenergy ) / maxflux; // normalize to 1
     //cout<<"interpolated max : "<<max<<", thisenergy : "<<thisenergy<<endl;
@@ -436,7 +443,7 @@ double  Spectra::GetNuEnergy() {
   } //while
   return pow(10.,thisenergy);
   }
-	
+
 } //Pick Neutrino Energy
 
 
@@ -490,13 +497,13 @@ inline void Spectra::GetFlux(string filename)
     cout<<"We are using "<<filename.c_str()<<" as the flux data."<<endl;
     cout<<"total lines in the file are "<<NLINES<<endl;
     E_bin = NLINES;
-    
+
 //    double flux[NLINES];//E2dNdE GeV cm^-2 s^-1 sr^-1
-    
+
     for(int i=0;i<NLINES;i++) {
         influx>>energy[i]>>E2dNdEdAdt[i];
     }
-    
+
     for(int i=0;i<E_bin;i++) {
 //        EdNdEdAdt[i]=pow(10.,(flux[i]+9.-energy[i]));
         EdNdEdAdt[i] = E2dNdEdAdt[i] + 9. - energy[i];  // change from GeV to eV and E2dN -> EdN
@@ -510,19 +517,19 @@ inline void Spectra::GetFlux(string filename)
 // TGraph *Spectra::GetGEdNdEdAdt() {
 //     return gEdNdEdAdt;
 // }
-// 
+//
 // TGraph *Spectra::GetGE2dNdEdAdt() {
 //     return gE2dNdEdAdt;
 // }
-// 
+//
 // TSpline3 *Spectra::GetSEdNdEdAdt() {
 //     return sEdNdEdAdt;
 // }
-// 
+//
 // TSpline3 *Spectra::GetSE2dNdEdAdt() {
 //     return sE2dNdEdAdt;
 // }
-//-------------------------------------------------- 
+//--------------------------------------------------
 
 double *Spectra::Getenergy() {
     return energy;
@@ -609,4 +616,3 @@ int Spectra::IsMonoenergetic() {
     }
     return out;
 }
-
diff --git a/data/atten_TB_paper_avg.txt b/data/atten_TB_paper_avg.txt
new file mode 100644
index 00000000..d6f49c48
--- /dev/null
+++ b/data/atten_TB_paper_avg.txt
@@ -0,0 +1,34 @@
+#Attenuation model in ice from https://arxiv.org/pdf/1105.2854.pdf, fig 23. Average attenuation length (blue line)
+2.76e+2, 2.61e+3
+3.25e+2, 2.53e+3
+3.76e+2, 2.45e+3
+4.32e+2, 2.36e+3
+4.93e+2, 2.28e+3
+5.58e+2, 2.20e+3
+6.24e+2, 2.12e+3
+6.92e+2, 2.04e+3
+7.64e+2, 1.95e+3
+8.38e+2, 1.87e+3
+9.11e+2, 1.79e+3
+9.84e+2, 1.71e+3
+1.06e+3, 1.63e+3
+1.13e+3, 1.55e+3
+1.20e+3, 1.47e+3
+1.27e+3, 1.38e+3
+1.33e+3, 1.30e+3
+1.40e+3, 1.22e+3
+1.46e+3, 1.14e+3
+1.51e+3, 1.06e+3
+1.56e+3, 9.78e+2
+1.61e+3, 8.96e+2
+1.66e+3, 8.13e+2
+1.71e+3, 7.31e+2
+1.75e+3, 6.50e+2
+1.78e+3, 5.70e+2
+1.82e+3, 4.87e+2
+1.86e+3, 4.04e+2
+1.89e+3, 3.20e+2
+1.92e+3, 2.39e+2
+1.96e+3, 1.56e+2
+1.99e+3, 7.24e+1
+2.02e+3, 7.66e+0
diff --git a/data/atten_TB_paper_lower.txt b/data/atten_TB_paper_lower.txt
new file mode 100644
index 00000000..17779608
--- /dev/null
+++ b/data/atten_TB_paper_lower.txt
@@ -0,0 +1,31 @@
+#Attenuation model in ice from https://arxiv.org/pdf/1105.2854.pdf, fig 23. Lower limit attenuation length
+3.28e+2, 2.60e+3
+3.91e+2, 2.51e+3
+4.55e+2, 2.42e+3
+5.15e+2, 2.35e+3
+6.01e+2, 2.25e+3
+6.94e+2, 2.14e+3
+7.71e+2, 2.07e+3
+8.46e+2, 1.99e+3
+9.46e+2, 1.89e+3
+1.03e+3, 1.82e+3
+1.11e+3, 1.74e+3
+1.18e+3, 1.67e+3
+1.26e+3, 1.59e+3
+1.36e+3, 1.49e+3
+1.45e+3, 1.39e+3
+1.55e+3, 1.29e+3
+1.63e+3, 1.19e+3
+1.71e+3, 1.10e+3
+1.79e+3, 9.96e+2
+1.87e+3, 8.87e+2
+1.92e+3, 8.02e+2
+1.98e+3, 7.12e+2
+2.03e+3, 6.25e+2
+2.07e+3, 5.37e+2
+2.12e+3, 4.43e+2
+2.16e+3, 3.55e+2
+2.20e+3, 2.81e+2
+2.25e+3, 1.67e+2
+2.29e+3, 8.31e+1
+2.33e+3, 5.23e+0
diff --git a/data/atten_TB_paper_upper.txt b/data/atten_TB_paper_upper.txt
new file mode 100644
index 00000000..8c0dbbe6
--- /dev/null
+++ b/data/atten_TB_paper_upper.txt
@@ -0,0 +1,29 @@
+#Attenuation model in ice from https://arxiv.org/pdf/1105.2854.pdf, fig 23. Upper limit attenuation length
+2.60e+2, 2.60e+3
+3.13e+2, 2.51e+3
+3.70e+2, 2.41e+3
+4.42e+2, 2.30e+3
+5.10e+2, 2.21e+3
+5.85e+2, 2.11e+3
+6.70e+2, 2.00e+3
+7.55e+2, 1.90e+3
+8.34e+2, 1.80e+3
+9.21e+2, 1.70e+3
+9.98e+2, 1.60e+3
+1.08e+3, 1.50e+3
+1.16e+3, 1.40e+3
+1.24e+3, 1.29e+3
+1.31e+3, 1.20e+3
+1.37e+3, 1.11e+3
+1.43e+3, 1.02e+3
+1.47e+3, 9.41e+2
+1.52e+3, 8.56e+2
+1.57e+3, 7.54e+2
+1.60e+3, 6.86e+2
+1.64e+3, 5.98e+2
+1.68e+3, 4.98e+2
+1.72e+3, 3.96e+2
+1.76e+3, 2.82e+2
+1.80e+3, 1.84e+2
+1.84e+3, 8.81e+1
+1.87e+3, 5.81e+0
diff --git a/data/coopersarkar_sigma_nu.csv b/data/coopersarkar_sigma_nu.csv
new file mode 100644
index 00000000..450a64b6
--- /dev/null
+++ b/data/coopersarkar_sigma_nu.csv
@@ -0,0 +1,31 @@
+50,0.32,4.1,-2.3,-2.4,0.1,3.8,-1.9,-2
+100,0.65,3.8,-2,-2,0.2,3.5,-1.8,-1.8
+200,1.3,3.5,-1.8,-1.9,0.41,3.2,-1.6,-1.7
+500,3.2,3.2,-1.7,-1.8,1,2.9,-1.5,-1.5
+1000,6.2,3,-1.6,-1.7,2,2.7,-1.4,-1.5
+2000,12,2.7,-1.6,-1.6,3.8,2.4,-1.3,-1.4
+5000,27,2.3,-1.5,-1.5,8.6,2.1,-1.3,-1.3
+10000,47,2,-1.4,-1.4,15,1.8,-1.2,-1.2
+20000,77,1.8,-1.3,-1.4,26,1.6,-1.1,-1.1
+50000,140,1.5,-1.2,-1.2,49,1.3,-1,-1.1
+100000,210,1.4,-1.2,-1.2,75,1.2,-1,-1
+200000,310,1.5,-1.1,-1.1,110,1.2,-0.9,-0.9
+500000,490,1.6,-1,-1,180,1.3,-0.8,-0.8
+1.00E+06,690,1.7,-0.9,-0.9,260,1.4,-0.8,-0.8
+2.00E+06,950,1.9,-0.9,-0.9,360,1.6,-0.8,-0.8
+5.00E+06,1400,2,-0.9,-0.9,540,1.8,-0.8,-0.8
+1.00E+07,1900,2.2,-0.9,-0.9,730,2,-0.8,-0.8
+2.00E+07,2600,2.3,-0.9,-1,980,2.2,-0.8,-0.9
+5.00E+07,3700,2.5,-0.9,-1.2,1400,2.4,-0.9,-1.1
+1.00E+08,4800,2.7,-0.9,-1.5,1900,2.6,-0.9,-1.3
+2.00E+08,6200,2.8,-1,-2,2400,2.7,-1,-1.8
+5.00E+08,8700,3,-1.1,-3,3400,2.9,-1,-2.6
+1.00E+09,11000,3.1,-1.2,-3.9,4400,3,-1.1,-3.4
+2.00E+09,14000,3.3,-1.2,-5,5600,3.2,-1.2,-4.4
+5.00E+09,19000,3.4,-1.4,-6.8,7600,3.4,-1.3,-6.1
+1.00E+10,24000,3.6,-1.5,-8.5,9600,3.5,-1.4,-7.6
+2.00E+10,30000,3.7,-1.6,-10.3,12000,3.6,-1.5,-9.3
+5.00E+10,39000,3.8,-1.7,-13.1,16000,3.8,-1.7,-11.8
+1.00E+11,48000,4,-1.8,-15.2,20000,3.9,-1.8,-13.9
+2.00E+11,59000,4.1,-1.9,-17.5,24000,4,-1.9,-16.1
+5.00E+11,75000,4.2,-2.0,-20.3,31000,4.2,-2.0,-18.8
\ No newline at end of file
diff --git a/data/coopersarkar_sigma_nubar.csv b/data/coopersarkar_sigma_nubar.csv
new file mode 100644
index 00000000..828e17d8
--- /dev/null
+++ b/data/coopersarkar_sigma_nubar.csv
@@ -0,0 +1,31 @@
+50,0.15,15,-9,-9,0.05,12,-6.4,-6.4
+100,0.33,13.3,-7.4,-7.4,0.12,10.7,-5.7,-5.7
+200,0.69,11.9,-6.5,-6.5,0.24,9.6,-5.1,-5.1
+500,1.8,10.5,-5.7,-5.7,0.61,8.6,-4.6,-4.6
+1000,3.6,9.4,-5.2,-5.2,1.2,7.8,-4.2,-4.2
+2000,7,8.3,-4.6,-4.6,2.4,7,-3.8,-3.8
+5000,17,6.5,-3.7,-3.7,5.8,5.7,-3.2,-3.2
+10000,31,5.1,-3,-3,11,4.6,-2.7,-2.7
+20000,55,3.8,-2.3,-2.3,19,3.6,-2.1,-2.1
+50000,110,2.5,-1.7,-1.7,39,2.4,-1.5,-1.5
+100000,180,1.9,-1.4,-1.4,64,1.7,-1.2,-1.2
+200000,270,1.7,-1.2,-1.2,99,1.4,-1,-1
+500000,460,1.7,-1.1,-1.1,170,1.4,-0.9,-0.9
+1.00E+06,660,1.8,-1,-1,240,1.5,-0.8,-0.8
+2.00E+06,920,1.9,-1,-1,350,1.6,-0.8,-0.8
+5.00E+06,1400,2.1,-0.9,-0.9,530,1.9,-0.8,-0.8
+1.00E+07,1900,2.2,-0.9,-0.9,730,2,-0.8,-0.8
+2.00E+07,2500,2.3,-0.9,-1,980,2.2,-0.8,-0.9
+5.00E+07,3700,2.5,-0.9,-1.2,1400,2.4,-0.9,-1.1
+1.00E+08,4800,2.7,-1,-1.5,1900,2.6,-0.9,-1.3
+2.00E+08,6200,2.8,-1,-2,2400,2.7,-1,-1.8
+5.00E+08,8700,3,-1.1,-3,3400,2.9,-1,-2.6
+1.00E+09,11000,3.1,-1.2,-3.9,4400,3,-1.1,-3.4
+2.00E+09,14000,3.3,-1.2,-5,5600,3.2,-1.2,-4.4
+5.00E+09,19000,3.4,-1.4,-6.8,7600,3.4,-1.3,-6.1
+1.00E+10,24000,3.6,-1.5,-8.5,9600,3.5,-1.4,-7.6
+2.00E+10,30000,3.7,-1.6,-10.3,12000,3.6,-1.5,-9.3
+5.00E+10,39000,3.8,-1.7,-13.1,16000,3.8,-1.7,-11.8
+1.00E+11,48000,4,-1.8,-15.2,20000,3.9,-1.8,-13.9
+2.00E+11,59000,4.1,-1.9,-17.5,24000,4,-1.9,-16.1
+5.00E+11,75000,4.2,-2.0,-20.3,31000,4.2,-2.0,-18.8
\ No newline at end of file
diff --git a/filter7pole600MHz.txt b/filter7pole600MHz.txt
new file mode 100644
index 00000000..6401c425
--- /dev/null
+++ b/filter7pole600MHz.txt
@@ -0,0 +1,60 @@
+83330000.000000    0.999531    
+99990000.000000    0.999390    
+116650000.000000    0.999234    
+133310000.000000    0.999062    
+149970000.000000    0.998873    
+166630000.000000    0.998668    
+183290000.000000    0.998443    
+199950000.000000    0.998200    
+216610000.000000    0.997936    
+233270000.000000    0.997650    
+249930000.000000    0.997338    
+266590000.000000    0.996998    
+283250000.000000    0.996621    
+299910000.000000    0.996197    
+316570000.000000    0.995704    
+333230000.000000    0.995105    
+349890000.000000    0.994336    
+366550000.000000    0.993290    
+383210000.000000    0.991792    
+399870000.000000    0.989559    
+416530000.000000    0.986147    
+433190000.000000    0.980883    
+449850000.000000    0.972766    
+466510000.000000    0.960372    
+483170000.000000    0.941786    
+499830000.000000    0.914615    
+516490000.000000    0.876203    
+533150000.000000    0.824154    
+549810000.000000    0.757243    
+566470000.000000    0.676422    
+583130000.000000    0.585408    
+599790000.000000    0.490266    
+616450000.000000    0.397892    
+633110000.000000    0.314115    
+649770000.000000    0.242475    
+666430000.000000    0.184069    
+683090000.000000    0.138138    
+699750000.000000    0.102946    
+716410000.000000    0.076457    
+733070000.000000    0.056743    
+749730000.000000    0.042161    
+766390000.000000    0.031403    
+783050000.000000    0.023470    
+799710000.000000    0.017612    
+816370000.000000    0.013273    
+833030000.000000    0.010049    
+849690000.000000    0.007643    
+866350000.000000    0.005841    
+883010000.000000    0.004484    
+899670000.000000    0.003458    
+916330000.000000    0.002679    
+932990000.000000    0.002085    
+949650000.000000    0.001629    
+966310000.000000    0.001278    
+982970000.000000    0.001007    
+999630000.000000    0.000797    
+1016290000.000000    0.000000    
+1032950000.000000    0.000000    
+1049610000.000000    0.000000    
+1066270000.000000    0.000000    
diff --git a/fluxes/Cuoco_CenA.dat b/fluxes/Cuoco_CenA.dat
new file mode 100644
index 00000000..0dc13f21
--- /dev/null
+++ b/fluxes/Cuoco_CenA.dat
@@ -0,0 +1,15 @@
+14
+15.188      -9.974
+15.392      -9.716
+15.587      -9.469
+15.983      -9.250
+16.489      -9.101
+16.984      -8.953
+17.489      -8.803
+17.984      -8.656
+18.490      -8.506
+18.984      -8.360
+19.490      -8.210
+19.985      -8.062
+20.495      -7.911
+20.974      -7.769
diff --git a/fluxes/Kotera2010_Fe_rich.dat b/fluxes/Kotera2010_Fe_rich.dat
index 09e245ce..f6cf7312 100644
--- a/fluxes/Kotera2010_Fe_rich.dat
+++ b/fluxes/Kotera2010_Fe_rich.dat
@@ -1,5 +1,5 @@
 21
-14.0054	-11.5952
+14.0054 -11.5952
 14.1573	-11.4549
 14.4069	-11.1848
 14.7649	-10.8523
diff --git a/fluxes/README b/fluxes/README
index ca9813b3..1c7a25a3 100644
--- a/fluxes/README
+++ b/fluxes/README
@@ -4,7 +4,7 @@ EXPONENT from 12 ~ 100 dat files are from Fenfang Wu in UC Irvine.
 Can add more models (EXPONENT >= 100 && EXPONENT < 200 is empty).
 
 In the file, first line is the number of data points,
-and from the second line, first column : energy in log, second column : flux E^2dN/dE [GeV/(cm^2*str*s)].
+and from the second line, first column : energy (in eV) in log, second column : flux E^2dN/dE [GeV/(cm^2*str*s)].
 
 32. essfig9.dat-----ESS's paper in Physical Review D, Volume 64, 093010 scaled(using fig4 for the ratio of nu_e/nu_mu) FIG 9 for nu_mu+nu_e
 
@@ -57,5 +57,5 @@ and from the second line, first column : energy in log, second column : flux E^2
 
 224. Kotera2010_max.dat-----Kotera flux max from ARA paper arXiv:1105.2854v1, Fig.27 Kotera et al. '10 max
 
-
+225. Cuoco_CenA.dat-------Cuoco et. al. flux from Centarurs A (Cen A). Fig 2, arXiv:0712.1830
 
diff --git a/log.txt b/log.txt
index db688e93..14c1a413 100644
--- a/log.txt
+++ b/log.txt
@@ -45,7 +45,7 @@ Also, we can change the center of pentagon array (core_x, core_y),
 distance between stations (station_spacing)
 
 In mode 1 : total number of stations (number_of_stations)
-            
+
 In mode 2 : number of stations on the side (stations_per_side)
 
 More detail will be shown on AraSim_doc.pdf file.
@@ -82,7 +82,7 @@ More detail, see AraSim_doc.pdf file.
     GetGain function in Detector -> use freq_step, ang_step, freq_width, freq_init in Detector instead of same values in Parameters class (it causes returning wrong vales... and I don't understand why)
 
 
-3) some other minor changes : 
+3) some other minor changes :
     Ray class : added WhereDoesItLeave function from icemc ray class
     EarthModel class : added TRandom3.h header file
     counting class : add from icemc (need for Primaries class)
@@ -498,7 +498,7 @@ AraRoot like output data in AraOut.root file.
 For that, if your machine doesn't have AraRoot installed, AraSim may not
 compile or run correctly.
 In that case, try to add new environment variables and try again.
-For example, you can add 
+For example, you can add
 
 export ARASIM_SYS=( the location where your AraSim is located )
 export LD_LIBRARY_PATH=$ARASIM_SYS/lib:$LD_LIBRARY_PATH
@@ -581,7 +581,7 @@ cout<<event->Nu_Interaction[0].changle;
 
 Fixed few bugs.
 
-1) fixed switched NC, CC mode. Previously in Primary class it recognized NC : 1 and CC : 0 index while the array (m_fsigma) to calculate the cross setion used opposite way. 
+1) fixed switched NC, CC mode. Previously in Primary class it recognized NC : 1 and CC : 0 index while the array (m_fsigma) to calculate the cross setion used opposite way.
 
 2) When we calcuate the weight (probability to survive to posnu), so far AraSim used either NC or CC cross section (depending on which interaction it
 is at posnu). Now when we calcuate the weight, AraSim uses the total cross section (NC + CC).
@@ -598,12 +598,12 @@ For example,
 
     noise_ID is a vector array as there could be more than 1 pure noise waveform used for trigger analysis (almost all cases it will be just one value, actually if there's more than one value, current AraSim can't handle that case correctly).
 
-    If above noise_ID value is 10, that means for that event, antenna, 
-    
+    If above noise_ID value is 10, that means for that event, antenna,
+
     trigger->v_noise_timedomain[ 10 ][ noise waveform data, size : settings->DATA_BIN_SIZE, default 16384 ]
 
     above pure noise waveform is used fot trigger analysis.
-    For the channels which passed the trigger (report->stations[i].strings[j].antennas[k].Trig_Pass is not 0), V_mimic waveform should used the pure noise waveform 
+    For the channels which passed the trigger (report->stations[i].strings[j].antennas[k].Trig_Pass is not 0), V_mimic waveform should used the pure noise waveform
 
     trigger->v_noise_timedomain[ noise_ID ][ 512 bins where Trig_Pass bin value is located at the center ]
 
@@ -741,7 +741,7 @@ By default, if you use different system temperature modes (NOISE_TEMP_MODE=1 or
 Additional to this difference, you can give an offset to the threshold to each channels.
 TRIG_THRES_MODE=0 will not give any threshold offset (default)
 TRIG_THRES_MODE=1 will read data/threshold_offset.csv file and apply those values to each channels. (ex. if the value for ch1 in csv file is 2, threshold will be rms_diode * powerthreshold * 2)
-TRIG_THRES_MODE=2 will not read data/threshold_offset.csv file but use the gain offset for each channels as threshold offset. (ex. if gain offset for ch1 is 2, threshold will be rms_diode * powerthreshold * 2^2) 
+TRIG_THRES_MODE=2 will not read data/threshold_offset.csv file but use the gain offset for each channels as threshold offset. (ex. if gain offset for ch1 is 2, threshold will be rms_diode * powerthreshold * 2^2)
 
 
 ===============================================================================
@@ -837,7 +837,7 @@ Added new NOISE mode. After obtaining the Rayleigh distribution fit from force t
 NOISE=0 uses just flat thermal noise spectrum from constant temperature and apply preamp, filter gains to them.
 NOISE=1 uses Rayleigh distribution bit value from TestBed data (distribution at different freq values) so don't use any preamp filter gain for noise waveforms.
 
-Currently NOISE=1 mode is available with 
+Currently NOISE=1 mode is available with
 DETECTOR=3
 READGEOM=1
 NOISE_TEMP_MODE=1 or 2
@@ -970,7 +970,7 @@ Massive update
 
 
 3) minor update : saturation in electronics chain is implemented.
-    
+
     V_SATURATION in setup wil set the limit voltage in degitized waveform.
     Degitized waveform values which have outside the range +-V_SATURATION will be forced to + or - V_SATURATION value.
     By default V_SATURATION = 1.0 which is 1.0 V or 1000 mV
@@ -1037,7 +1037,7 @@ Like old Calpulser mode, currently Calpulser mode will work only with DETECTOR=3
 Added ability to define output directory for argc==4, at argv[3]
 added inverse exponential index of refraction model with NOFZ=2
 added conditional dependence on AraRoot for AraRoot-like output
-	checks if ARA_UTIL_INSTALL_DIR exists and links against the libraries there to make a UsefulIcrrStationEvent 
+	checks if ARA_UTIL_INSTALL_DIR exists and links against the libraries there to make a UsefulIcrrStationEvent
 
 ===============================================================================
 
@@ -1122,22 +1122,22 @@ AraOut.setup.txt.run0.root instead of AraOut.setupdirectory/setup.txt.run0.root
 
 * can now add third parameter to AraSim for output directory:
 
-./AraSim setup.txt 0 /path/to/output/dir/ 
+./AraSim setup.txt 0 /path/to/output/dir/
 
 can add slash in the end or not
 
 * in Spectra.cc : added new EXPONENT values between 510 and 650 (including), so we can have non-integer energy values:
 
-the formula is E=10^X with X=(EXPONENT-400)/10 
+the formula is E=10^X with X=(EXPONENT-400)/10
 
 so if you want 10^18.3eV use EXPONENT=400+18.3*10=583
 
-added a bash script to make a dynamic load library "library.sh"  
-run it and get "libSim.so" which is useful for loading all the simulation files you need to link with. 
+added a bash script to make a dynamic load library "library.sh"
+run it and get "libSim.so" which is useful for loading all the simulation files you need to link with.
 
-added the user guide in its own directory. 
+added the user guide in its own directory.
 
-modified the StandardDefinitions.mk : commented out the parts where it calls ARA_UTIL_INSTALL_DIR 
+modified the StandardDefinitions.mk : commented out the parts where it calls ARA_UTIL_INSTALL_DIR
 (it messed up my installation and I think in general AraRoot conflicts with AraSim)
 
 
@@ -1151,10 +1151,10 @@ Triggering upgrade:
 
 -in TRIG_SCAN_MODE=0 triggering works same as before (default)
 -in TRIG_SCAN_MODE=1 triggering is faster using circular buffer (10-15% for time domain, 40-50% for freq domain)
--in TRIG_SCAN_MODE=2 choose low POWERTHRESHOLD, for each triggered event get above what Pthresh this would trigger (e.g. event can trigger if threshold was -5.7). 
--results for mode 2 saved in report->stations[].TDR_all and TDR_Hpol and TDR_Vpol and sorted from highest to lowest in TDR_Vpol_sorted etc. (TDR= Tunnel Diode Response). 
+-in TRIG_SCAN_MODE=2 choose low POWERTHRESHOLD, for each triggered event get above what Pthresh this would trigger (e.g. event can trigger if threshold was -5.7).
+-results for mode 2 saved in report->stations[].TDR_all and TDR_Hpol and TDR_Vpol and sorted from highest to lowest in TDR_Vpol_sorted etc. (TDR= Tunnel Diode Response).
 
-So for one run at TRIG_SCAN_MODE=2 and POWERTHRESHOLD=-4 and TRIG_MODE=1 (trigger on Hpol and Vpol seperately) and N_TRIG_H=N_TRIG_V=3 we will get for each event the maximum number of channels and maximum POWERTHRESHOLD combination on which it would trigger (e.g. it could trigger at -6.1 in 3 channels or -5.9 at 4 channels). Don't need to run different runs for different Pthresh or N_TRIG, can make the cuts out of the outputfile. 
+So for one run at TRIG_SCAN_MODE=2 and POWERTHRESHOLD=-4 and TRIG_MODE=1 (trigger on Hpol and Vpol seperately) and N_TRIG_H=N_TRIG_V=3 we will get for each event the maximum number of channels and maximum POWERTHRESHOLD combination on which it would trigger (e.g. it could trigger at -6.1 in 3 channels or -5.9 at 4 channels). Don't need to run different runs for different Pthresh or N_TRIG, can make the cuts out of the outputfile.
 
 
 ============================================================================
@@ -1169,7 +1169,7 @@ So for one run at TRIG_SCAN_MODE=2 and POWERTHRESHOLD=-4 and TRIG_MODE=1 (trigge
 04/24/14 Eugene Hong;
 
 Added new ARA measured Ice Attenuation factor mode.
-Settings, 
+Settings,
 USE_ARA_ICEATTENU=1
 uses new ARA measured Ice Attenuation length (300MHz value across entire frequencies).
 Also it uses ray trace steps information to account different attenuation length as a function of depth.
@@ -1185,9 +1185,9 @@ To go back to old method, use USE_ARA_ICEATTENU=0
 
 Added new sigma (neutrino cross section) boundary values.
 When we use Connolly et al 2011 (http://arxiv.org/abs/1102.0691, Fig1, Fig2 plots and Table 3 and 4 for parameter values) cross section mode (SIGMAPARAM=1),
-We can use mean cross section (by default) with 
-Settings, 
-SIGMA_SELECT=0 
+We can use mean cross section (by default) with
+Settings,
+SIGMA_SELECT=0
 
 and upper bound value by
 SIGMA_SELECT=1
@@ -1248,13 +1248,13 @@ So Veff/Aeff will be simply decided by INTERACTION_MODE=1 or 0.
 
 06/23/14 Guy Nir:
 
-Added SingleChannelTriggers to Antenna_r in Report class. Saves the total number of triggers in each channel. 
-Added SCT_threshold_pass Antenna_r in Report class. A vector of the Pthresh values for each single channel trigger. 
-Added TRIG_SCAN_MODE=3 to settings, that tells AraSim to fill SCT_threshold_pass with values. 
+Added SingleChannelTriggers to Antenna_r in Report class. Saves the total number of triggers in each channel.
+Added SCT_threshold_pass Antenna_r in Report class. A vector of the Pthresh values for each single channel trigger.
+Added TRIG_SCAN_MODE=3 to settings, that tells AraSim to fill SCT_threshold_pass with values.
 
-Added OUTPUT_TDR_GRAPH to settings, which tells AraSim to save some tunnel diode output waveforms, for debugging. 
+Added OUTPUT_TDR_GRAPH to settings, which tells AraSim to save some tunnel diode output waveforms, for debugging.
 
-Added TGraph *getWaveform(...) function to Report class, to get the waveforms from V_mimic and time_mimic vectors. 
+Added TGraph *getWaveform(...) function to Report class, to get the waveforms from V_mimic and time_mimic vectors.
 
 ============================================================================
 
@@ -1266,9 +1266,9 @@ I am still working to confirm the effective area mode is working properly.
 
 07/08/14 Guy Nir:
 
-Added Interaction::clear_useless() method to clear the shower profile vectors. 
+Added Interaction::clear_useless() method to clear the shower profile vectors.
 These vectors took a very large volume in the output files, especially when saving all events.
-This only applies in DATA_SAVE_MODE>0. 
+This only applies in DATA_SAVE_MODE>0.
 
 ============================================================================
 
@@ -1333,8 +1333,6 @@ removed useless/problematic option in makefile
 added namespace definition in Tools.h
 
 ============================================================================
-<<<<<<< .working
-
 04/07/2017 Carl Pfendner:
 
 Added option to import geometry from AraRoot for stations 2, 3 - use
@@ -1410,11 +1408,11 @@ See Settings.h for more details
 
 10/12/2017 Carl Pfendner:
 
-Added APPLY_NOISE_FIGURE mode to settings to attempt to include the calibration information from Thomas 
+Added APPLY_NOISE_FIGURE mode to settings to attempt to include the calibration information from Thomas
 WARNING!!: this is incomplete as of this edit. The channel dependent
 noise figures do not work correctly yet.
 Added ANTENNA_MODE mode to settings to allow for new antenna models to
-be imported 
+be imported
 The newest mode allows the use of a separate antenna model for the top
 VPol antennas in the layout.
 
@@ -1495,13 +1493,45 @@ Added flexible antennas_per_string and strings_per_station to setup file read-in
 Cleanup tabs in the Tools class, including the removal of several deprecated functions
 which are not used anywhere else in AraSim currently
 
-// static void SimpleLinearInterpolation_extend_180cut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 ); 
-// static void SimpleLinearInterpolation_extend_PIcut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 ); 
-// static void SimpleLinearInterpolation_OutZero_180cut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 ); 
+// static void SimpleLinearInterpolation_extend_180cut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 );
+// static void SimpleLinearInterpolation_extend_PIcut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 );
+// static void SimpleLinearInterpolation_OutZero_180cut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 );
 // static void SimpleLinearInterpolation_OutZero_PIcut(int n1, double *x1, double *y1, int n2, double *x2, double *y2 );
 
 
 Also clean-up tabs in Vector class
+============================================================================
+
+2019/12/12 Brian Clark
+
+- Cleanup Settings class with correct tabs
+
+- Add DETECTOR_STATION_LIVETIME_CONFIG, which allows for configuration selection when run in detector 2/3 mode
+  =0 is default (do nothing special)
+  =1,2,3,4,5 are the five configs from the A2/A3 4yr analysis
+  >5 is not supported currently and will throw an error
+  will also throw an error if attempt to use for stations besides 2 and 3
+
+- in Report.h and Report.cc add triggerDelay and mostDelay variables, and fill them correctly, for when we need
+  to adjust triggering and readout parameters
+
+- additionally, add trigger masking to Report.cc when in ==0 trig mode ("old" mode) for emulating station a2 in configs >2
+
+============================================================================
+
+2019/12/19
+
+In the a23_4yr_diffuse branch, added feature to estimate signal chain efficiency uncertainty. The uncertainty is represented as a scale-down of the antenna gains consisting of a 600MHz low-pass filter and a drop in gain values by 10% and 32% for Vpol and Hpol, respectively.
+
+Three Settings paramters are added:
+- USE_SIGNAL_CHAIN_LOWER_BOUND: default 0 -  pre-scaling antenna gains, the default AraSim values. 1 - scale the gains to produce lower bound values as described above.
+- SC_EFFICIENCY_ERROR_V: default 0.9 - the gain drop for Vpol to be used when USE_SIGNAL_CHAIN_LOWER_BOUND=1
+- SC_EFFICIENCY_ERROR_H: default 0.68 - the gain drop for Vpol to be used when USE_SIGNAL_CHAIN_LOWER_BOUND=1
+
+One data file is added:
+- filter7pole600MHz.txt: 600MHz low-pass curve data (vs freq)
+
+============================================================================
 
 2019/12/21 Ming-Yuan Lu
 
@@ -1511,6 +1541,42 @@ Split Settings::CheckCompatibilities function to two - one that does not require
 The former is moved to be called right after the setup file is read, which spares having to instantiate all class objects before 
 we even check parameter compatibility. The latter is left as is.
 
+============================================================================
+
+2020/01/14 Jorge Torres
+
+In the a23_4yr_diffuse branch, added feature to estimate signal chain efficiency uncertainty. The uncertainty is represented as a scale-down of the antenna gains consisting of a 600MHz low-pass filter and a drop in gain values by 10% and 32% for Vpol and Hpol, respectively.
+
+- Added the parameter SYSTEMATICS_IceAtten. The default value is zero, which uses Eugene's attenuation model (http://radiorm.physics.ohio-state.edu/elog/Write-Ups/170504_105713/Thesis_-_Eugene_Hong.pdf, p. 54), red line.
+Values 1 and 2 are used for lower and upper bound, respectively. The values are hardcoded in the IceModel class.
+
+============================================================================
+
+
 2020/01/15 Ming-Yuan Lu
 Rename overloaded Settings::CheckCompatibilities functions to Settings::CheckCompatibilitiesSettings() & Settings::CheckCompatibilitiesDetector(Detector *detector) to avoid confusion.
+============================================================================
+2020/01/24 Ming-Yuan Lu
+Initialize Settings::DETECTOR_STATION to be 2, and Settings::DETECTOR_STATION_LIVETIME_CONFIG to be 0
+============================================================================
+
+2020/01/27 Brian Clark
+Add SYSTEMATICS_nofz to wiggle RAY_TRACE_ICE_MODEL_PARAMS within uncertainties.
+=0=default fit values
+=1=make larger by uncertainties
+=2=make smaller by uncertainties
+
+============================================================================
+
+
+2020/03/15 Brian Clark
+Add Cooper-Sarkar cross-section model. Activated by using SIGMAPARAM=2.
 
+Also, add two new SIGMA_SELECT modes (3 and 4) for use with SIGMAPARAM=1.
+Modes 3 and 4 allow you to use the upper and lower bounds (respectively)
+from Cooper-Sarkar, but apply them to the Connolly cross-section calculation.
+So, if SIGMAPARAM=1 and SIGMA_SELECT=3, then the cross-section used will
+be the Connolly cross section, but increased by the upper bound uncertainty
+as computed by Cooper-Sarkar. This is a "hack" to see what happens to
+the Connolly result if you assume the Cooper-Sarkar uncertainties
+which are smaller than those derived in Connolly et. al.
\ No newline at end of file
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