#include <iostream>
#include <thread>
#include <chrono>
#include <cmath>


using namespace std;

void nap(){
  // usleep(3000);
  // this_thread::sleep_for(30000ms);

  for (int i=0;i<1000000000;i++){
    double j = sqrt(i^2);
  }
}

int main(){

  cout << "taking a nap" << endl;

  nap();

  cout << "hello world" << endl;

}

SHELL=/bin/sh

# Note: Comments start with #.  $(FOOBAR) means: evaluate the variable 
#        defined by FOOBAR= (something).

# This file contains a set of rules used by the "make" command.
#   This makefile $(MAKEFILE) tells "make" how the executable $(COMMAND) 
#   should be create from the source files $(SRCS) and the header files 
#   $(HDRS) via the object files $(OBJS); type the command:
#        "make -f make_program"
#   where make_program should be replaced by the name of the makefile.
# 
# Programmer:  Dick Furnstahl (furnstahl.1@osu.edu)
# Latest revision: 12-Jan-2016 
# 
# Notes:
#  * If you are ok with the default options for compiling and linking, you
#     only need to change the entries in section 1.
#
#  * Defining BASE determines the name for the makefile (prepend "make_"), 
#     executable (append ".x"), zip archive (append ".zip") and gzipped 
#     tar file (append ".tar.gz"). 
#
#  * To remove the executable and object files, type the command:
#          "make -f $(MAKEFILE) clean"
#
#  * To create a zip archive with name $(BASE).zip containing this 
#     makefile and the SRCS and HDRS files, type the command:
#        "make -f $(MAKEFILE) zip"
#
#  * To create a gzipped tar file with name $(BASE).tar.gz containing this 
#     makefile and the source and header files, type the command:
#          "make -f $(MAKEFILE) tarz"
#
#  * Continuation lines are indicated by \ with no space after it.  
#     If you get a "missing separator" error, it is probably because there
#     is a space after a \ somewhere.
#

###########################################################################
# 1. Specify base name, source files, header files, input files
########################################################################### 

# The base for the names of the makefile, executable command, etc.
BASE= hello_world

# Put all C++ (or other) source files here.  NO SPACES after continuation \'s.
SRCS= \
hello_world.cpp

# Put all header files here.  NO SPACES after continuation \'s.
HDRS= \

# Put any input files you want to be saved in tarballs (e.g., sample files).
INPFILE= \

###########################################################################
# 2. Generate names for object files, makefile, command to execute, tar file
########################################################################### 

# *** YOU should not edit these lines unless to change naming conventions ***

OBJS= $(addsuffix .o, $(basename $(SRCS)))
MAKEFILE= make_$(BASE)
COMMAND=  $(BASE).x
TARFILE= $(BASE).tar.gz
ZIPFILE= $(BASE).zip

###########################################################################
# 3. Commands and options for different compilers
########################################################################### 

#
# Compiler parameters
#
# CXX           Name of the C++ compiler to use
# CFLAGS        Flags to the C++ compiler
# CWARNS        Warning options for C++ compiler
# F90           Name of the fortran compiler to use (if relevant) 
# FFLAGS        Flags to the fortran compiler 
# LDFLAGS       Flags to the loader
# LIBS          A list of libraries 
#

CXX= g++
CFLAGS=  -g
CWARNS= -Wall -W -Wshadow -fno-common 
MOREFLAGS= -Wpedantic -Wpointer-arith -Wcast-qual -Wcast-align \
           -Wwrite-strings -fshort-enums 

# add relevant libraries and link options
LIBS=           
# LDFLAGS= -lgsl -lgslcblas 
LDFLAGS=

###########################################################################
# 4. Instructions to compile and link, with dependencies
########################################################################### 
all:    $(COMMAND) 

.SUFFIXES:
.SUFFIXES: .o .mod .f90 .f .cpp

#%.o:   %.mod 

# This is the command to link all of the object files together. 
#  For fortran, replace CXX by F90.
$(COMMAND): $(OBJS) $(MAKEFILE) 
	$(CXX) -o $(COMMAND) $(OBJS) $(LDFLAGS) $(LIBS)

# Command to make object (.o) files from C++ source files (assumed to be .cpp).
#  Add $(MOREFLAGS) if you want additional warning options.
%.o: %.cpp $(HDRS) $(MAKEFILE)
	$(CXX) -c $(CFLAGS) $(CWARNS) -o $@ $<

# Commands to make object (.o) files from Fortran-90 (or beyond) and
#  Fortran-77 source files (.f90 and .f, respectively).
.f90.mod:
	$(F90) -c $(F90FLAGS) -o $@ $< 
 
.f90.o: 
	$(F90) -c $(F90FLAGS) -o $@ $<
 
.f.o:   
	$(F90) -c $(FFLAGS) -o $@ $<
      
##########################################################################
# 5. Additional tasks      
##########################################################################
      
# Delete the program and the object files (and any module files)
clean:
	/bin/rm -f $(COMMAND) $(OBJS)
	/bin/rm -f $(MODIR)/*.mod
 
# Pack up the code in a compressed gnu tar file 
tarz:
	tar cfvz $(TARFILE) $(MAKEFILE) $(SRCS) $(HDRS) $(MODIR) $(INPFILE) 

# Pack up the code in a zip archive
zip:
	zip -r $(ZIPFILE) $(MAKEFILE) $(SRCS) $(HDRS) $(MODIR) $(INPFILE) 

##########################################################################
# That's all, folks!     
##########################################################################

#include "TF1.h"

void fitSnr();

void fitSnr()

{
	gStyle->SetLineWidth(4); //set some style parameters
	TFile *stripe1file = new TFile("hstripe1snr.root"); //import the file containing the histogram to be fit
	TH1D *hstripe1 = (TH1D*)stripe1file->Get("stripe1snr"); //get the histogram to be fit
	TCanvas c1("c1","c1",1000,800); //make a canvas
	hstripe1->Draw(""); //draw it
	c1.SetLogy(); //set a log axis

	//need to declare an equation
	//I want to fit for two paramters, in the equation these are [0] and [1]
	//so, you'll need to re-write the equation to whatever you're trying to fit for
	//but ROOT wants the variables to find to be given as [0], [1], [2], etc.
	
	char equation1[150]; //declare a container for the equation
	sprintf(equation1,"([0]*(x^[1]))"); //declare the equation
	TF1 *fit1 = new TF1("PowerFit",equation1,20,50); //create a function to fit with, with the range being 20 to 50

	//now, we need to set the initial parameters of the fit
	//fit->SetParameter(0,H->GetRMS()); //this should be a good starting place for a standard deviation like variable
	//fit->SetParameter(1,H->GetMaximum()); //this should be a good starting place for amplitude like variable
	fit1->SetParameter(0,60000.); //for our example, we will manually choose this
	fit1->SetParameter(1,-3.);

	hstripe1->Fit("PowerFit","R"); //actually do the fit;
	fit1->Draw("same"); //draw the fit

	//now, we want to print out some parameters to see how good the fit was
	cout << "par0 " << fit1->GetParameter(0) << " par1 " << fit1->GetParameter(1) << endl;
	cout<<"chisquare "<<fit1->GetChisquare()<<endl;
	cout<<"Ndf "<<fit1->GetNDF()<<endl;
	cout<<"reduced chisquare "<<double(fit1->GetChisquare())/double(fit1->GetNDF())<<endl;
	cout<<"   "<<endl;
	c1.SaveAs("stripe1snrfit.png");

}

export ROOTSYS=/users/PAS0174/osu8620/root-6.08.06
eval 'source /users/PAS0174/osu8620/root-6.08.06/builddir/bin/thisroot.sh'
export LD_INCLUDE_PATH=/users/PAS0174/osu8620/cint/libcint/build/include:$LD_INCLUDE_PATH
module load fftw3/3.3.5
module load gnu/6.3.0
module load python/3.4.2
module load cmake/3.7.2

#might need this, but probably not
#export CC=/usr/local/gcc/6.3.0/bin/gcc

Notes

#First we need to read in the data
dataSim <- read.table("output.txt.Simulation",sep=" ",header=TRUE)
dataRF <- read.table("output.txt.RFTriggers",sep=" ",header=TRUE)
dataPulser <- read.table("output.txt.CalPulsers",sep=" ",header=TRUE)

#Now we combine them into one data object
data <- rbind(dataRF,dataSim)

#Now we actually have to specify that we
#want to use the first 10 columns
data <- data[,1:10]

#make a principal component analysis object
pca <- prcomp(data,center=TRUE,scale=TRUE,retx=TRUE)

#Load a plotting library
library(ggfortify)

#then can plot
autplot(prcomp(data))

#or, we can plot like this
#to get some color data points
labels<-c(rep(0,nrow(dataSim)),rep(1,nrow(dataRF)))
plot(pca$x[,1],pca$x[,2],col=labels+1)

#we can also do an LDA analysis

#we need to import the MASS library
library(MASS)
#and now we make the lda object
lda(data,grouping=labels)

#didn't write down any plotting unfortunately.

////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////		plot_event.cxx 
////		plot deep station event
////
////		Apr 2018,  clark.2668@osu.edu
////////////////////////////////////////////////////////////////////////////////

//Includes
#include <iostream>

//AraRoot Includes
#include "RawAtriStationEvent.h"
#include "UsefulAtriStationEvent.h"
#include "AraEventCalibrator.h"

//ROOT Includes
#include "TTree.h"
#include "TFile.h"
#include "TGraph.h"
#include "TCanvas.h"

using namespace std;

int main(int argc, char **argv)
{
	
	//check to make sure they've given me a run and a pedestal
	if(argc<2) {
		std::cout << "Usage\n" << argv[0] << " <run file>\n";
		std::cout << "e.g.\n" << argv[0] << " event1841.root\n";
		return 0;
	}
  
	char pedFileName[200];
	sprintf(pedFileName, "%s", argv[1]);
  
	printf("------------------------------------------------------------------------\n");
	printf("%s\n", argv[0]);
	printf("runFileName %s\n", argv[1]);
	printf("------------------------------------------------------------------------\n");
	
	
	TFile *fp = TFile::Open(argv[2]);
	if(!fp) {
		std::cerr << "Can't open file\n";
		return -1;
	}
	TTree *eventTree = (TTree*) fp->Get("eventTree");
	if(!eventTree) {
		std::cerr << "Can't find eventTree\n";
		return -1;
	}
		
	RawAtriStationEvent *rawAtriEvPtr = 0; //empty pointer	   
	eventTree->SetBranchAddress("event",&rawAtriEvPtr); //set the branch address
	Int_t run_num; //run number of event
	eventTree->SetBranchAddress("run", &run_num); //set the branch address
	
	int numEntries=eventTree->GetEntries(); //get the number of events
	int stationId=0;
	eventTree->GetEntry(0);
	stationId = rawAtriEvPtr->stationId; //assign the statio id number
		
	AraEventCalibrator *calib = AraEventCalibrator::Instance(); //make a calibrator

	for(int event=0;event<numEntries;event++) {
	//for(int event=0;event<700;event++) {
		
		eventTree->GetEntry(event); //get the event
		int evt_num = rawAtriEvPtr->eventNumber; //check the event umber
		if(rawAtriEvPtr->isCalpulserEvent()==0) continue; //bounce out if it's not a cal pulser
		UsefulAtriStationEvent *realAtriEvPtr_fullcalib = new UsefulAtriStationEvent(rawAtriEvPtr, AraCalType::kLatestCalib); //make the event

		TGraph *waveforms[16]={0};
		for(int i=0; i<16; i++){
			waveforms[i]=realAtriEvPtr_fullcalib->getGraphFromRFChan(i);
		}
		TCanvas *canvas = new TCanvas("","",1000,1000);
		canvas->Divide(4,4);
		for(int i=0; i<16; i++){
			canvas->cd(i+1);
			waveforms[i]->Draw("alp");
		}
		char title[200];
		sprintf(title,"waveforms_run%d_event%d.pdf",stationId,run_num,evt_num);
		canvas->SaveAs(title);
		delete canvas;		
	}	
}

#include <iostream>
#include <fstream>
#include <sstream>
#include <math.h>
#include <string>
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <time.h>
#include <cstdio>
#include <cstdlib>
#include <unistd.h>
#include <cstring>
#include <unistd.h>

#include "TTreeIndex.h"
#include "TChain.h"
#include "TFile.h"
#include "TTree.h"
#include "TMath.h"

#include "Event.h"
#include "Detector.h"
#include "Report.h"
#include "Vector.h"
#include "counting.hh"

using namespace std;

//Get effective volumes with error bars

class EarthModel;

int main(int argc, char **argv)
{
	gStyle->SetOptStat(111111);
	gStyle->SetOptDate(1);
	
	if(argc<4){
		cout<<"Not enough arguments! Abort run."<<endl;
		cout<<"Run like: ./veff volradius voldepth AraOut1.root AraOut2.rot ..."<<endl;
		return -1;
	}

	double volradius = atof(argv[1]);
	double voldepth = atof(argv[2]);

	TChain *AraTree = new TChain("AraTree");
	TChain *AraTree2 = new TChain("AraTree2");

	for(int i=3; i<argc;i++){
		AraTree->Add(string(argv[i]).c_str());
		AraTree2->Add(string(argv[i]).c_str());
	}

	Report *report = 0;
	Event *event=0;
	AraTree2->SetBranchAddress("report",&report);
	AraTree2->SetBranchAddress("event",&event);

	int totnthrown = AraTree2->GetEntries();
	cout << "Total number of events: " << totnthrown << endl;

	int NBINS=10;
	double eventsfound_binned[NBINS];
	for(int i=0; i<NBINS; i++) eventsfound_binned[i]=0.;

	double totweight=0;
	for(int iEvt2=0; iEvt2<totnthrown; iEvt2++){
		AraTree2->GetEntry(iEvt2);
		if(report->stations[0].Global_Pass<=0) continue;
		double weight = event->Nu_Interaction[0].weight;
		if(weight > 1.0) continue;
		totweight += weight;

		int index_weights = Counting::findWeightBin(log10(weight));
		if(index_weights<NBINS) eventsfound_binned[index_weights]++;
	}

	double error_minus=0.;
	double error_plus=0.;
	Counting::findErrorOnSumWeights(eventsfound_binned,error_plus,error_minus);

	double vtot = TMath::Pi() * double(volradius) * double(volradius) * double(voldepth) / 1.e9; //answer in km^3
	double veff = vtot * totweight / double(totnthrown) * 4. * TMath::Pi(); //answer in km^3 sr
	double veff_p  = vtot * (error_plus) / double(totnthrown) * 4. * TMath::Pi(); //answer in km^3 sr
	double veff_m  = vtot * (error_minus) / double(totnthrown) * 4. * TMath::Pi(); //answer in km^3 sr
                                                                                                                          
	printf("volthrown: %.6f \n  totweight: %.6f + %.6f - %.6f \n  Veff: %.6f + %.6f - %.6f \n",
			vtot,
			totweight, error_plus, error_minus,
			veff, veff_p, veff_m
			);
	return 0;
}

#############################################################################
##
##Changes:
##line 54 - OBJS = .... add filename.o      .... del oldfilename.o
##line 55 - CCFILE = .... add filename.cc     .... del oldfilename.cc
##line 58 - PROGRAMS = filename
##line 62 - filename : $(OBJS)
##
##############################################################################
include StandardDefinitions.mk

#Site Specific  Flags
ifeq ($(strip $(BOOST_ROOT)),)
	BOOST_ROOT = /usr/local/include
endif
SYSINCLUDES	= -I/usr/include -I$(BOOST_ROOT)
SYSLIBS         = -L/usr/lib
DLLSUF = ${DllSuf}
OBJSUF = ${ObjSuf}
SRCSUF = ${SrcSuf}

CXX = g++

#Generic and Site Specific Flags
CXXFLAGS     += $(INC_ARA_UTIL) $(SYSINCLUDES) 
LDFLAGS      += -g $(LD_ARA_UTIL) -I$(BOOST_ROOT) $(ROOTLDFLAGS) -L. 

# copy from ray_solver_makefile (removed -lAra part)

# added for Fortran to C++

LIBS	= $(ROOTLIBS) -lMinuit $(SYSLIBS) 
GLIBS	= $(ROOTGLIBS) $(SYSLIBS)


LIB_DIR = ./lib
INC_DIR = ./include

#ROOT_LIBRARY = libAra.${DLLSUF}

OBJS = Vector.o EarthModel.o IceModel.o Trigger.o Ray.o Tools.o Efficiencies.o Event.o Detector.o Position.o Spectra.o RayTrace.o RayTrace_IceModels.o signal.o secondaries.o Settings.o Primaries.o counting.o RaySolver.o Report.o eventSimDict.o veff.o
CCFILE = Vector.cc EarthModel.cc IceModel.cc Trigger.cc Ray.cc Tools.cc Efficiencies.cc Event.cc Detector.cc Spectra.cc Position.cc RayTrace.cc signal.cc secondaries.cc RayTrace_IceModels.cc Settings.cc Primaries.cc counting.cc RaySolver.cc Report.cc veff.cc
CLASS_HEADERS = Trigger.h Detector.h Settings.h Spectra.h IceModel.h Primaries.h Report.h Event.h secondaries.hh #need to add headers which added to Tree Branch

PROGRAMS = veff

all : $(PROGRAMS) 
	
veff : $(OBJS)
	$(LD) $(OBJS) $(LDFLAGS)  $(LIBS) -o $(PROGRAMS) 
	@echo "done."

#The library
$(ROOT_LIBRARY) : $(LIB_OBJS) 
	@echo "Linking $@ ..."
ifeq ($(PLATFORM),macosx)
# We need to make both the .dylib and the .so
		$(LD) $(SOFLAGS)$@ $(LDFLAGS) $(G77LDFLAGS) $^ $(OutPutOpt) $@
ifneq ($(subst $(MACOSX_MINOR),,1234),1234)
ifeq ($(MACOSX_MINOR),4)
		ln -sf $@ $(subst .$(DllSuf),.so,$@)
else
		$(LD) -dynamiclib -undefined $(UNDEFOPT) $(LDFLAGS) $(G77LDFLAGS) $^ \
		   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)
endif
endif
else
	$(LD) $(SOFLAGS) $(LDFLAGS) $(G77LDFLAGS) $(LIBS) $(LIB_OBJS) -o $@
endif

##-bundle

#%.$(OBJSUF) : %.$(SRCSUF)
#	@echo "<**Compiling**> "$<
#	$(CXX) $(CXXFLAGS) -c $< -o  $@

%.$(OBJSUF) : %.C
	@echo "<**Compiling**> "$<
	$(CXX) $(CXXFLAGS) $ -c $< -o  $@

%.$(OBJSUF) : %.cc
	@echo "<**Compiling**> "$<
	$(CXX) $(CXXFLAGS) $ -c $< -o  $@

# added for fortran code compiling
%.$(OBJSUF) : %.f
	@echo "<**Compiling**> "$<
	$(G77) -c $<


eventSimDict.C: $(CLASS_HEADERS)
	@echo "Generating dictionary ..."
	@ rm -f *Dict* 
	rootcint $@ -c ${INC_ARA_UTIL} $(CLASS_HEADERS) ${ARA_ROOT_HEADERS} LinkDef.h

clean:
	@rm -f *Dict*
	@rm -f *.${OBJSUF}
	@rm -f $(LIBRARY)
	@rm -f $(ROOT_LIBRARY)
	@rm -f $(subst .$(DLLSUF),.so,$(ROOT_LIBRARY))	
	@rm -f $(TEST)
#############################################################################

///////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
///////		demo.cxx
//////		Nov 2018, Brian Clark 
//////		Demonstrate how to draw 2 TH2D's with two different color palettes (needs ROOT6)
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////

//C++
#include <iostream>

//ROOT Includes
#include "TH2D.h"
#include "TCanvas.h"
#include "TStyle.h"
#include "TExec.h"
#include "TColor.h"
#include "TPaletteAxis.h"
#include "TRandom3.h"

using namespace std;

int main(int argc, char **argv)
{

	gStyle->SetOptStat(0);

	TH2D *h1 = new TH2D("h1","h1",100,-10,10,100,-10,10);
	TH2D *h2 = new TH2D("h2","h2",100,-10,10,100,-10,10);

	TRandom3 *R = new TRandom3(time(0));
	int count=0;
	while(count<10000000){
		h1->Fill(R->Gaus(-4.,1.),R->Gaus(-4.,1.));
		count++;
	}

	TRandom3 *R2 = new TRandom3(time(0)+100);
	count=0;
	while(count<10000000){
		h2->Fill(R2->Gaus(4.,1.),R2->Gaus(4.,1.));
		count++;
	}

	TCanvas *c = new TCanvas("c","c",1100,850);

	h1->Draw("colz");
		TExec *ex1 = new TExec("ex1","gStyle->SetPalette(kValentine);");
		ex1->Draw();
		h1->Draw("colz same");
	gPad->SetLogz();
	gPad->Modified();
	gPad->Update();

	TPaletteAxis *palette1 = (TPaletteAxis*)h1->GetListOfFunctions()->FindObject("palette");
	palette1->SetX1NDC(0.7);
	palette1->SetX2NDC(0.75);
	palette1->SetY1NDC(0.1);
	palette1->SetY2NDC(0.95);

	gPad->SetRightMargin(0.3);
	gPad->SetTopMargin(0.05);

	h2->Draw("same colz");
		TExec *ex2 = new TExec("ex2","gStyle->SetPalette(kCopper);"); //TColor::InvertPalette();
		ex2->Draw();
		h2->Draw("same colz");
	gPad->SetLogz();
	gPad->Modified();
	gPad->Update();

	TPaletteAxis *palette2 = (TPaletteAxis*)h2->GetListOfFunctions()->FindObject("palette");
	palette2->SetX1NDC(0.85);
	palette2->SetX2NDC(0.90);
	palette2->SetY1NDC(0.1);
	palette2->SetY2NDC(0.95);

	h1->SetTitle("");
	h1->GetXaxis()->SetTitle("X-Value");
	h1->GetYaxis()->SetTitle("Y-Value");

	h1->GetZaxis()->SetTitle("First Histogram Events");
	h2->GetZaxis()->SetTitle("Second Histogram Events");

	h1->GetYaxis()->SetTitleSize(0.05);
	h1->GetXaxis()->SetTitleSize(0.05);
	h1->GetYaxis()->SetLabelSize(0.045);
	h1->GetXaxis()->SetLabelSize(0.045);

	h1->GetZaxis()->SetTitleSize(0.045);
	h2->GetZaxis()->SetTitleSize(0.045);
	h1->GetZaxis()->SetLabelSize(0.04);
	h2->GetZaxis()->SetLabelSize(0.04);
	
	h1->GetYaxis()->SetTitleOffset(1);
	h1->GetZaxis()->SetTitleOffset(1);
	h2->GetZaxis()->SetTitleOffset(1);

	c->SetLogz();
	c->SaveAs("test.png");

}

LDFLAGS=-L${ARA_UTIL_INSTALL_DIR}/lib -L${shell root-config --libdir}
CXXFLAGS=-I${ARA_UTIL_INSTALL_DIR}/include -I${shell root-config --incdir}
LDLIBS += $(shell $(ROOTSYS)/bin/root-config --libs)

////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////  demo.cxx 
////  demo
////
////  Nov 2018
////////////////////////////////////////////////////////////////////////////////

//Includes
#include <iostream>
#include <string>
#include <sstream>

//AraRoot Includes
#include "RawAtriStationEvent.h"
#include "UsefulAtriStationEvent.h"

//ROOT Includes
#include "TTree.h"
#include "TFile.h"
#include "TGraph.h"

using namespace std;

RawAtriStationEvent *rawAtriEvPtr;

int main(int argc, char **argv)
{

	if(argc<3) {
		std::cout << "Usage\n" << argv[0] << " <input_file> <output_location> "<<endl;
		return -1;
	}

	/*
	arguments
	0: exec
	1: input data file
	2: output location
	*/
	
	TFile *fpIn = TFile::Open(argv[1]);
	if(!fpIn) {
		std::cout << "Can't open file\n";
		return -1;
	}
	TTree *eventTree = (TTree*) fpIn->Get("eventTree");
	if(!eventTree) {
		std::cout << "Can't find eventTree\n";
		return -1;
	}
	eventTree->SetBranchAddress("event",&rawAtriEvPtr);
	int run;
	eventTree->SetBranchAddress("run",&run);
	eventTree->GetEntry(0);
	printf("Filter Run Number %d \n", run);

	char outfile_name[400];
	sprintf(outfile_name,"%s/outputs_run%d.root",argv[2],run);

	TFile *fpOut = TFile::Open(outfile_name, "RECREATE");
	TTree* outTree = new TTree("outTree", "outTree");
	int WaveformLength[16];
	outTree->Branch("WaveformLength", &WaveformLength, "WaveformLength[16]/D");
	
	Long64_t numEntries=eventTree->GetEntries();

	for(Long64_t event=0;event<numEntries;event++) {
		eventTree->GetEntry(event);
		UsefulAtriStationEvent *realAtriEvPtr = new UsefulAtriStationEvent(rawAtriEvPtr, AraCalType::kLatestCalib);
		for(int i=0; i<16; i++){
			TGraph *gr = realAtriEvPtr->getGraphFromRFChan(i);
			WaveformLength[i] = gr->GetN();
			delete gr;
		}		
		outTree->Fill();
		delete realAtriEvPtr;
	} //loop over events
	
	fpOut->Write();
	fpOut->Close();
	
	fpIn->Close();
	delete fpIn;
}

#/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l mem=4GB
#PBS -l walltime=00:05:00
#PBS -A PAS0654
#PBS -e /fs/scratch/PAS0654/shell_demo/err_out_logs
#PBS -o /fs/scratch/PAS0654/shell_demo/err_out_logs

# you should change the -e and -o to write your 
# log files to a location of your preference

# source your own shell script here
eval 'source /users/PAS0654/osu0673/A23_analysis/env.sh'

# $RUNDIR was defined in the submission script 
# along with $FILE and $OUTPUTDIR

cd $RUNDIR

# $TMPDIR is the local memory of this specific node
# it's the only variable we didn't have to define

./bin/demo $FILE $TMPDIR 

# after we're done
# we copy the results to the $OUTPUTDIR

pbsdcp $TMPDIR/'*.root' $OUTPUTDIR

/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1000.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1001.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1002.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1004.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1005.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1006.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1007.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1009.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1010.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1011.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1012.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1014.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1015.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1016.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1017.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1019.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1020.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1021.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1022.root
/fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event1024.root

#!/bin/bash

#where should the outputs be stored?
OutputDir="/fs/scratch/PAS0654/shell_demo/outputs"
echo '[ Processed file output directory: ' $OutputDir ' ]'
export OutputDir

#where is your executable compiled?
RunDir="/users/PAS0654/osu0673/A23_analysis/araROOT"
export RunDir

#define the list of runs to execute on
readfile=run_list.txt

counter=0
while read line1
do
	qsub -v RUNDIR=$RunDir,OUTPUTDIR=$OutputDir,FILE=$line1 -N 'job_'$counter run.sh
	counter=$((counter+1))
done < $readfile

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
        . ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/.local/bin:$HOME/bin

export PATH

# .bashrc

source bashrc_anita.sh

# we also want to set two more environment variables that ANITA needs
# you should update ICEMC_SRC_DIR and ICEMC_BUILD_DIR to wherever you
# downloaded icemc too

export ICEMC_SRC_DIR=/path/to/icemc #change this line!
export ICEMC_BUILD_DIR=/path/to/icemc #change this line!
export DYLD_LIBRARY_PATH=${ICEMC_SRC_DIR}:${ICEMC_BUILD_DIR}:${DYLD_LIBRARY_PATH}

//C++ includes
#include <iostream>

//ROOT includes
#include "TCanvas.h"
#include "TStyle.h"
#include "TH1D.h"
#include "TFile.h"
#include "TTree.h"

using namespace std;

int main(int argc, char *argv[])
{

	if(argc<2)
	{
		cout << "Not enough arguments! Stop run. " << endl;
		return -1;
	}

	/*
	we're going to make a histogram, and set some parameters about it's X and Y axes
	*/
	TH1D *nuflavorint_hist = new TH1D("nuflavorint", "",3,1,4);  
	nuflavorint_hist->SetTitle("Neutrino Flavors");
	nuflavorint_hist->GetXaxis()->SetTitle("Neutrino Flavors (1=e, 2=muon, 3=tau)");
	nuflavorint_hist->GetYaxis()->SetTitle("Weigthed Fraction of Total Detected Events");
	nuflavorint_hist->GetXaxis()->SetTitleOffset(1.2);
	nuflavorint_hist->GetYaxis()->SetTitleOffset(1.2);
	nuflavorint_hist->GetXaxis()->CenterTitle();
	nuflavorint_hist->GetYaxis()->CenterTitle();

	for(int i=1; i < argc; i++)
		
	{  // loop over the input files

		//now we are going to load the icefinal.root file and draw in the "passing_events" tree, which stores info
		
		string readfile = string(argv[i]);
		TFile *AnitaFile = new TFile(( readfile ).c_str());
		cout << "AnitaFile" << endl;
		TTree *passing_events = (TTree*)AnitaFile->Get("passing_events");
		cout << "Reading AnitaFile..." << endl;

		//declare three variables we are going to use later
		
		int num_pass;               // number of entries (ultra-neutrinos);
		double weight;              // weight of neutrino counts;
		int nuflavorint;              // neutrino flavors;
		
		num_pass = passing_events->GetEntries();
		cout << "num_pass is " << num_pass << endl;
		
		/*PRIMARIES VARIABLES*/

		//set the "branch" of the tree which stores specific pieces of information
		
		passing_events->SetBranchAddress("weight", &weight);
		passing_events->SetBranchAddress("nuflavor", &nuflavorint);

		//loop over all the events in the tree
	
		for (int k=0; k <=num_pass; k++)
		{
			passing_events->GetEvent(k);
			nuflavorint_hist->Fill(nuflavorint, weight); //fill the histogram with this value and this weight
		
		} // CLOSE FOR LOOP OVER NUMBER OF EVENTS
		
	} // CLOSE FOR LOOP OVER NUMBER OF INPUT FILES

	//set up some parameters to make things loo pretty
	gStyle->SetHistFillColor(0);
	gStyle->SetHistFillStyle(1);
	gStyle->SetHistLineColor(1);
	gStyle->SetHistLineStyle(0);
	gStyle->SetHistLineWidth(2.5); //Setup plot Style

	//make a "canvas" to draw on

	TCanvas *c4 = new TCanvas("c4", "nuflavorint", 1100,850);
	gStyle->SetOptTitle(1);
	gStyle->SetStatX(0.33);
	gStyle->SetStatY(0.87);
	nuflavorint_hist->Draw("HIST"); //draw on it
			
	//Save Plots
	
	//make the line thicker and then save the result
	gStyle->SetHistLineWidth(9);
	c4->SaveAs("nuflavorint.png");
	gStyle->SetHistLineWidth(2);
	c4->SaveAs("nuflavorint.pdf");

	delete c4; //clean up
	return 0; //return successfully
	
}

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

module load cmake/3.11.4
module load gnu/7.3.0
export CC=`which gcc`
export CXX=`which g++`

export BOOST_ROOT=/fs/project/PAS0654/shared_software/anita/owens_pitzer/build/boost_build
export LD_LIBRARY_PATH=${BOOST_ROOT}/stage/lib:$LD_LIBRARY_PATH
export BOOST_LIB=$BOOST_ROOT/stage/lib
export LD_LIBRARY_PATH=$BOOST_LIB:$LD_LIBRARY_PATH

export ROOTSYS=/fs/project/PAS0654/shared_software/anita/owens_pitzer/build/root
eval 'source /fs/project/PAS0654/shared_software/anita/owens_pitzer/build/root/bin/thisroot.sh'

# Makefile for the ROOT test programs.  # This Makefile shows nicely how to compile and link applications
# using the ROOT libraries on all supported platforms.
#
# Copyright (c) 2000 Rene Brun and Fons Rademakers
#
# Author: Fons Rademakers, 29/2/2000

include Makefile.arch

################################################################################
# Site specific flags
################################################################################
# Toggle these as needed to get things to install

#BOOSTFLAGS = -I boost_1_48_0
# commented out for kingbee and older versions of gcc
ANITA3_EVENTREADER=1

# Uncomment to enable healpix 
#USE_HEALPIX=1

# Uncomment to disable explicit vectorization (but will do nothing if ANITA_UTIL is not available) 
#VECTORIZE=1


# The ROOT flags are added to the CXXFLAGS in the .arch file
# so this should be simpler...
ifeq (,$(findstring -std=, $(CXXFLAGS)))
	ifeq ($(shell test $(GCC_MAJOR) -lt 5; echo $$?),0)
		ifeq ($(shell test $(GCC_MINOR) -lt 5; echo $$?),0)
			CXXFLAGS += -std=c++0x
		else
			CXXFLAGS += -std=c++11
		endif
	endif
endif

################################################################################

# If not compiling with C++11 (or later) support, all occurrences of "constexpr"
# must be replaced with "const", because "constexpr" is a keyword
# which pre-C++11 compilers do not support.
# ("constexpr" is needed in the code to perform in-class initialization
# of static non-integral member objects, i.e.:
#		static const double c_light = 2.99e8;
# which works in C++03 compilers, must be modified to:
#		static constexpr double c_light = 2.99e8;
# to work in C++11, but adding "constexpr" breaks C++03 compatibility.
# The following compiler flag defines a preprocessor macro which is
# simply:
#		#define constexpr const
# which replaces all instances of the text "constexpr" and replaces it
# with "const".
# This preserves functionality while only affecting very specific semantics.

ifeq (,$(findstring -std=c++1, $(CXXFLAGS)))
	CPPSTD_FLAGS = -Dconstexpr=const
endif



# Uses the standard ANITA environment variable to figure
# out if ANITA libs are installed
ifdef ANITA_UTIL_INSTALL_DIR
	ANITA_UTIL_EXISTS=1
	ANITA_UTIL_LIB_DIR=${ANITA_UTIL_INSTALL_DIR}/lib
	ANITA_UTIL_INC_DIR=${ANITA_UTIL_INSTALL_DIR}/include
	LD_ANITA_UTIL=-L$(ANITA_UTIL_LIB_DIR)
	LIBS_ANITA_UTIL=-lAnitaEvent -lRootFftwWrapper
	INC_ANITA_UTIL=-I$(ANITA_UTIL_INC_DIR)
	ANITA_UTIL_ETC_DIR=$(ANITA_UTIL_INSTALL_DIR)/etc
endif

ifdef ANITA_UTIL_EXISTS
	CXXFLAGS += -DANITA_UTIL_EXISTS
endif

ifdef VECTORIZE
	CXXFLAGS += -DVECTORIZE -march=native -fabi-version=0
endif

ifdef ANITA3_EVENTREADER
	CXXFLAGS += -DANITA3_EVENTREADER
endif

ifdef USE_HEALPIX
	CXXFLAGS += -DUSE_HEALPIX `pkg-config --cflags healpix_cxx`
	LIBS  += `pkg-config --libs healpix_cxx` 
endif


################################################################################

GENERAL_FLAGS = -g -O2 -pipe -m64 -pthread
WARN_FLAGS = -W -Wall -Wextra -Woverloaded-virtual
# -Wno-unused-variable -Wno-unused-parameter -Wno-unused-but-set-variable

CXXFLAGS += $(GENERAL_FLAGS) $(CPPSTD_FLAGS) $(WARN_FLAGS) $(ROOTCFLAGS) $(INC_ANITA_UTIL)

DBGFLAGS  = -pipe -Wall -W -Woverloaded-virtual -g -ggdb -O0 -fno-inline

DBGCXXFLAGS = $(DBGFLAGS) $(ROOTCFLAGS) $(BOOSTFLAGS)
LDFLAGS  += $(CPPSTD_FLAGS) $(LD_ANITA_UTIL) -I$(BOOST_ROOT) -L.
LIBS += $(LIBS_ANITA_UTIL)

# Mathmore not included in the standard ROOT libs
LIBS += -lMathMore

DICT = classdict

OBJS = vector.o position.o earthmodel.o balloon.o icemodel.o signal.o ray.o Spectra.o anita.o roughness.o secondaries.o Primaries.o Tools.o counting.o $(DICT).o Settings.o Taumodel.o screen.o GlobalTrigger.o ChanTrigger.o SimulatedSignal.o EnvironmentVariable.o source.o  random.o

BINARIES = test_plot$(ExeSuf)

################################################################################

.SUFFIXES: .$(SrcSuf) .$(ObjSuf) .$(DllSuf)

all:            $(BINARIES)

$(BINARIES): %: %.$(SrcSuf) $(OBJS)
		$(LD) $(CXXFLAGS) $(LDFLAGS) $(OBJS) $< $(LIBS) $(OutPutOpt) $@
		@echo "$@ done"


.PHONY: clean
clean:
		@rm -f $(BINARIES)


%.$(ObjSuf) : %.$(SrcSuf) %.h
	@echo "<**Compiling**> "$<
	$(LD) $(CXXFLAGS) -c $< -o $@

#include <iostream>
#include <fstream>
#include <sstream>
#include <math.h>
#include <string>
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <time.h>
#include <cstdio>
#include <cstdlib>
#include <unistd.h>
#include <cstring>
#include <unistd.h>

#include "TTreeIndex.h"
#include "TChain.h"
#include "TH1.h"
#include "TF1.h"
#include "TF2.h"
#include "TFile.h"
#include "TRandom.h"
#include "TRandom2.h"
#include "TRandom3.h"
#include "TTree.h"
#include "TLegend.h"
#include "TLine.h"
#include "TROOT.h"
#include "TPostScript.h"
#include "TCanvas.h"
#include "TH2F.h"
#include "TText.h"
#include "TProfile.h"
#include "TGraphErrors.h"
#include "TStyle.h"
#include "TMath.h"
#include "TVector3.h"
#include "TRotation.h"
#include "TSpline.h"
#include "Math/InterpolationTypes.h"
#include "Math/Interpolator.h"
#include "Math/Integrator.h"
#include "TGaxis.h"
#include "TPaveStats.h"
#include "TLatex.h"

#include "Constants.h"
#include "Settings.h"
#include "Position.h"
#include "EarthModel.h"
#include "Tools.h"
#include "Vector.h"
#include "IceModel.h"
#include "Trigger.h"
#include "Spectra.h"
#include "signal.hh"
#include "secondaries.hh"
#include "Ray.h"
#include "counting.hh"
#include "Primaries.h"
#include "Efficiencies.h"
#include "Event.h"
#include "Detector.h"
#include "Report.h"

using namespace std;

/////////////////Plotting Script for nuflavorint for AraSIMQC
/////////////////Created by Kaeli Hughes, modified by Brian Clark
/////////////////Prepared on April 28 2016 as an "introductor script" to plotting with AraSim; for new users of queenbee

class EarthModel;

int main(int argc, char **argv)
{
	gStyle->SetOptStat(111111); //this is a selection of statistics settings; you should do some googling and figure out exactly what this particular comibation does
	gStyle->SetOptDate(1); //this tells root to put a date and timestamp on whatever plot we output
	
	if(argc<2){ //if you don't have at least 1 file to run over, then you haven't given it a file to analyze; this checks this
		cout<<"Not enough arguments! Abort run."<<endl;
	}
	
	//Create the histogram
		
	TCanvas *c2 = new TCanvas("c2", "nuflavorint", 1100,850); //make a canvas on which to plot the data
	TH1F *nuflavorint_hist = new TH1F("nuflavorint_hist", "nuflavorint histogram", 3, 0.5, 3.5); //create a histogram with three bins
	nuflavorint_hist->GetXaxis()->SetNdivisions(3); //set the number of divisions

	
	int total_thrown=0; // a variable to hold the grant total number of events thrown for all input files

	
	for(int i=1; i<argc;i++){ //loop over the input files
		
		string readfile; //create a variable called readfile that will hold the title of the simulation file
		readfile = string(argv[i]); //set the readfile variable equal to the filename
		
		Event *event = 0; //create a Event class pointer called event; note that it is set equal to zero to avoid creating a bald pointer
		Report *report=0; //create a Event class pointer called event; note that it is set equal to zero to avoid creating a bald pointer
		Settings *settings = 0; //create a Event class pointer called event; note that it is set equal to zero to avoid creating a bald pointer

		TFile *AraFile=new TFile(( readfile ).c_str()); //make a new file called "AraFile" that will be simulation file we are reading in

		if(!(AraFile->IsOpen())) return 0; //checking to see if the file we're trying to read in opened correctly; if not, bounce out of the program
			
		int num_pass;//number of passing events 
		
		TTree *AraTree=(TTree*)AraFile->Get("AraTree"); //get the AraTree
		TTree *AraTree2=(TTree*)AraFile->Get("AraTree2"); //get the AraTree2
		AraTree2->SetBranchAddress("event",&event); //get the event branch
		AraTree2->SetBranchAddress("report",&report); //get the report branch
		AraTree->SetBranchAddress("settings",&settings); //get the settings branch
		
		num_pass=AraTree2->GetEntries(); //get the number of passed events in the data file
		
		AraTree->GetEvent(0); //get the first event; sometimes the tree does not instantiate properly if you'd explicitly "active" the first event
		total_thrown+=(settings->NNU); //add the number of events from this file (The NNU variable) to the grand total; NNU is the number of THROWN neutrinos
		
		
		for (int k=0; k<num_pass; k++){ //going to fill the histograms for as many events as were in this input file
			
			AraTree2->GetEvent(k); //get the even from the tree

			int nuflavorint; //make the container variable
			double weight; //the weight of the event
			int trigger; //the global trigger value for the event

			
			nuflavorint=event->nuflavorint; //draw the event out; one of the objects in the event class is the nuflavorint, and this is the syntax for accessing it
			weight=event->Nu_Interaction[0].weight; //draw out the weight of the event
			
			trigger=report->stations[0].Global_Pass; //find out if the event was a triggered event or not
			
			/*				
			if(trigger!=0){ //check if the event triggered
				nuflavorint_hist->Fill(nuflavorint,weight); //fill the event into the histogram; the first argument of the fill (which is mandatory) is the value you're putting into the histogram; the second value is optional, and is the weight of the event in the histogram
				//in this particular version of the code then, we are only plotting the TRIGGERED events; if you wanted to plot all of the events, you could instead remove this "if" condition and just Fill everything
			}
			*/
			nuflavorint_hist->Fill(nuflavorint,weight); //fill the event into the histogram; the first argument of the fill (which is mandatory)	  
	}
				 
}
	//After looping over all the files, make the plots and save them
	

	//do some stuff to get the "total events thrown" text box ready; this is useful because on the plot itself you can then see how many events you THREW into the simulation; this is especially useful if you're only plotting passed events, but want to know what fraction of your total thrown that is
		char *buffer= (char*) malloc (250); //declare a buffer pointer, and allocate it some chunk of memory
		int a = snprintf(buffer, 250,"Total Events Thrown: %d",total_thrown); //print the words "Total Events Thrown: %d" to the variable "buffer" and tell the system how long that phrase is; the %d sign tells C++ to replace that "%d" with the next argument, or in this case, the number "total_thrown"
			if(a>=250){ //if the phrase is longer than the pre-allocated space, increase the size of the buffer until it's big enough
				buffer=(char*) realloc(buffer, a+1);
				snprintf(buffer, 250,"Total Events Thrown: %d",total_thrown);
				}
		TLatex *u = new TLatex(.3,.01,buffer); //create a latex tex object which we can draw on the cavas
		u->SetNDC(kTRUE); //changes the coordinate system for the tex object plotting
		u->SetIndiceSize(.1); //set the size of the latex index
		u->SetTextSize(.025); //set the size of the latex text

	nuflavorint_hist->Draw(); //draw the histogram
	nuflavorint_hist->GetXaxis()->SetTitle("Neutrino Flavor"); //set the x-axis label
	nuflavorint_hist->GetYaxis()->SetTitle("Number of Events (weighted)"); //set the y-axis label
	nuflavorint_hist->GetYaxis()->SetTitleOffset(1.5); //set the separation between the y-axis and it's label; root natively makes this smaller than is ideal
	nuflavorint_hist->SetLineColor(kBlack); //set the color of the histogram to black, instead of root's default navy blue
	u->Draw(); //draw the statistics box information

	c2->SaveAs("outputs/plotting_example.png"); //save the canvas as a JPG file for viewing
	c2->SaveAs("outputs/plotting_example.pdf"); //save the canvas as a PDF file for viewing
	c2->SaveAs("outputs/plotting_example.root"); //save the canvas as a ROOT file for viewing or editing later


}	//end main; this is the end of the script

#############################################################################
## Makefile -- New Version of my Makefile that works on both linux
##              and mac os x
## Ryan Nichol <rjn@hep.ucl.ac.uk>
##############################################################################
##############################################################################
##############################################################################
##
##This file was copied from M.readGeom and altered for my use 14 May 2014
##Khalida Hendricks.
##
##Modified by Brian Clark for use on plotting_example on 28 April 2016
##
##Changes:
##line 54 - OBJS = .... add filename.o      .... del oldfilename.o
##line 55 - CCFILE = .... add filename.cc     .... del oldfilename.cc
##line 58 - PROGRAMS = filename
##line 62 - filename : $(OBJS)
##
##
##############################################################################
##############################################################################
##############################################################################
include StandardDefinitions.mk

#Site Specific  Flags
ifeq ($(strip $(BOOST_ROOT)),)
	BOOST_ROOT = /usr/local/include
endif
SYSINCLUDES	= -I/usr/include -I$(BOOST_ROOT)
SYSLIBS         = -L/usr/lib
DLLSUF = ${DllSuf}
OBJSUF = ${ObjSuf}
SRCSUF = ${SrcSuf}

CXX = g++

#Generic and Site Specific Flags
CXXFLAGS     += $(INC_ARA_UTIL) $(SYSINCLUDES) 
LDFLAGS      += -g $(LD_ARA_UTIL) -I$(BOOST_ROOT) $(ROOTLDFLAGS) -L. 

# copy from ray_solver_makefile (removed -lAra part)

# added for Fortran to C++


LIBS	= $(ROOTLIBS) -lMinuit $(SYSLIBS) 
GLIBS	= $(ROOTGLIBS) $(SYSLIBS)


LIB_DIR = ./lib
INC_DIR = ./include

#ROOT_LIBRARY = libAra.${DLLSUF}

OBJS = Vector.o EarthModel.o IceModel.o Trigger.o Ray.o Tools.o Efficiencies.o Event.o Detector.o Position.o Spectra.o RayTrace.o RayTrace_IceModels.o signal.o secondaries.o Settings.o Primaries.o counting.o RaySolver.o Report.o eventSimDict.o plotting_example.o
CCFILE = Vector.cc EarthModel.cc IceModel.cc Trigger.cc Ray.cc Tools.cc Efficiencies.cc Event.cc Detector.cc Spectra.cc Position.cc RayTrace.cc signal.cc secondaries.cc RayTrace_IceModels.cc Settings.cc Primaries.cc counting.cc RaySolver.cc Report.cc plotting_example.cc
CLASS_HEADERS = Trigger.h Detector.h Settings.h Spectra.h IceModel.h Primaries.h Report.h Event.h secondaries.hh #need to add headers which added to Tree Branch

PROGRAMS = plotting_example

all : $(PROGRAMS) 
	
plotting_example : $(OBJS)
	$(LD) $(OBJS) $(LDFLAGS)  $(LIBS) -o $(PROGRAMS) 
	@echo "done."

#The library
$(ROOT_LIBRARY) : $(LIB_OBJS) 
	@echo "Linking $@ ..."
ifeq ($(PLATFORM),macosx)
# We need to make both the .dylib and the .so
		$(LD) $(SOFLAGS)$@ $(LDFLAGS) $(G77LDFLAGS) $^ $(OutPutOpt) $@
ifneq ($(subst $(MACOSX_MINOR),,1234),1234)
ifeq ($(MACOSX_MINOR),4)
		ln -sf $@ $(subst .$(DllSuf),.so,$@)
else
		$(LD) -dynamiclib -undefined $(UNDEFOPT) $(LDFLAGS) $(G77LDFLAGS) $^ \
		   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)
endif
endif
else
	$(LD) $(SOFLAGS) $(LDFLAGS) $(G77LDFLAGS) $(LIBS) $(LIB_OBJS) -o $@
endif

##-bundle

#%.$(OBJSUF) : %.$(SRCSUF)
#	@echo "<**Compiling**> "$<
#	$(CXX) $(CXXFLAGS) -c $< -o  $@

%.$(OBJSUF) : %.C
	@echo "<**Compiling**> "$<
	$(CXX) $(CXXFLAGS) $ -c $< -o  $@

%.$(OBJSUF) : %.cc
	@echo "<**Compiling**> "$<
	$(CXX) $(CXXFLAGS) $ -c $< -o  $@

# added for fortran code compiling
%.$(OBJSUF) : %.f
	@echo "<**Compiling**> "$<
	$(G77) -c $<


eventSimDict.C: $(CLASS_HEADERS)
	@echo "Generating dictionary ..."
	@ rm -f *Dict* 
	rootcint $@ -c ${INC_ARA_UTIL} $(CLASS_HEADERS) ${ARA_ROOT_HEADERS} LinkDef.h

clean:
	@rm -f *Dict*
	@rm -f *.${OBJSUF}
	@rm -f $(LIBRARY)
	@rm -f $(ROOT_LIBRARY)
	@rm -f $(subst .$(DLLSUF),.so,$(ROOT_LIBRARY))	
	@rm -f $(TEST)
#############################################################################

NFOUR=1024

EXPONENT=21
NNU=300 // number of neutrino events
NNU_PASSED=10 // number of neutrino events that are allowed to pass the trigger
ONLY_PASSED_EVENTS=0 // 0 (default): AraSim throws NNU events whether or not they pass; 1: AraSim throws events until the number of events that pass the trigger is equal to NNU_PASSED (WARNING: may cause long run times if reasonable values are not chosen)
NOISE_WAVEFORM_GENERATE_MODE=0 // generate new noise waveforms for each events
NOISE_EVENTS=16 // number of pure noise waveforms
TRIG_ANALYSIS_MODE=0 // 0 = signal + noise, 1 = signal only, 2 = noise only
DETECTOR=1 // ARA stations 1 to 7
NOFZ=1
core_x=10000
core_y=10000

TIMESTEP=5.E-10 // value for 2GHz actual station value
TRIG_WINDOW=1.E-7 // 100ns which is actual testbed trig window
POWERTHRESHOLD=-6.06 // 100Hz global trig rate for 3 out of 16 ARA stations

POSNU_RADIUS=3000
V_MIMIC_MODE=0 // 0 : global trig is located center of readout windows
DATA_SAVE_MODE=0 // 2 : don't save any waveform informations at all
DATA_LIKE_OUTPUT=0 // 0 : don't save any waveform information to eventTree
BORE_HOLE_ANTENNA_LAYOUT=0
SECONDARIES=0

TRIG_ONLY_BH_ON=0
CALPULSER_ON=0
USE_MANUAL_GAINOFFSET=0
USE_TESTBED_RFCM_ON=0
NOISE_TEMP_MODE=0
TRIG_THRES_MODE=0
READGEOM=0 // reads geometry information from the sqlite file or not (0 : don't read)

TRIG_MODE=0 // use vpol, hpol separated trigger mode. by default N_TRIG_V=3, N_TRIG_H=3. You can change this values

number_of_stations=1
core_x=10000
core_y=10000

DETECTOR=1
DETECTOR_STATION=2
DATA_LIKE_OUTPUT=0

NOISE_WAVEFORM_GENERATE_MODE=0 // generates new waveforms for every event
NOISE=0 //flat thermal noise
NOISE_CHANNEL_MODE=0 //using different noise temperature for each channel
NOISE_EVENTS=16 // number of noise events which will be store in the trigger class for later use

ANTENNA_MODE=1
APPLY_NOISE_FIGURE=0

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

module load cmake/3.11.4
module load gnu/7.3.0
export CC=`which gcc`
export CXX=`which g++`

export BOOST_ROOT=/fs/project/PAS0654/shared_software/anita/owens_pitzer/build/boost_build
export LD_LIBRARY_PATH=${BOOST_ROOT}/stage/lib:$LD_LIBRARY_PATH
export BOOST_LIB=$BOOST_ROOT/stage/lib
export LD_LIBRARY_PATH=$BOOST_LIB:$LD_LIBRARY_PATH

export ROOTSYS=/fs/project/PAS0654/shared_software/anita/owens_pitzer/build/root
eval 'source /fs/project/PAS0654/shared_software/anita/owens_pitzer/build/root/bin/thisroot.sh'

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
        . ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/.local/bin:$HOME/bin

export PATH

# .bashrc

source bashrc_anita.sh

# we also want to set two more environment variables that ANITA needs
# you should update ICEMC_SRC_DIR and ICEMC_BUILD_DIR to wherever you
# downloaded icemc too

export ICEMC_SRC_DIR=/path/to/icemc #change this line!
export ICEMC_BUILD_DIR=/path/to/icemc #change this line!
export DYLD_LIBRARY_PATH=${ICEMC_SRC_DIR}:${ICEMC_BUILD_DIR}:${DYLD_LIBRARY_PATH}