Merge branch 'master' of 192.168.1.2:/usr/local/git/wmu/phy-4660

accelerator/data/.Rhistory

@@ -1,72 +1,512 @@
-data1=read.table("0302171.tab",header=T)
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(2,at=189.12,"189.12")
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+?axis
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,hadj=1)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+e")
+> abline(h = 3700,col="purple",lwd=1)
+> abline(v = 203.63,col="purple",lwd=1)
+e")
+> abline(h = 3700,col="purple",lwd=1)
+> abline(v = 203.63,col="purple",lwd=1)
+e")
+> abline(h = 3700,col="purple",lwd=1)
+> abline(v = 203.63,col="purple",lwd=1)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,vadj=1)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+?axis
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1.3)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1.3)
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.3)
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1.3,"189.12±0.6")
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.3,"203.63±0.6")
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1.5,"189.12±0.6")
+axis(3,at=189.12,"0.352±0.009 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.5,"203.63±0.6")
+axis(3,at=203.63,"0.96±0.04 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
 plot(data1)
-data2=read.table("0302172.tab",header=T)
+plot(data2,type='l',xlim=c(185,205))
-lines(data2)
+lines(c(0,1023),c(7600,7600),col="blue")
-lines(data1)
+abline(h = 1520,col="blue",lwd=1)
-plot()
+abline(v = 189.12,col="blue",lwd=1)
-lines(data1)
+axis(1,at=189.12,padj=1.5,"189.12±0.6")
-sdfklj
+axis(3,at=189.12,"1.706±0.05 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.5,"203.63±0.6")
+axis(3,at=203.63,"1.838±0.05 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=4.5,height=3)
+203.63-189.12
+1.838-1.706
+.132/14.51
+1.706-.009*189.12
+energy_coords=data1$channel*.009+.00392
+energy_coords
+data2$energy=energy_coords
+plot(energy~count,data=data2)
+plot(count~energy,data=data2)
+data3$energy=energy_coords
+data1$energy=energy_coords
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0))
+plot(count~energy,data=data1,type='l')
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100),xlab="energy [MeV]")
+plot(pnorm(50,500)
+plot(pnorm(50,500))
+plot(dnorm(50,50,500))
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100),xlab="energy [MeV]")
+abline(v = 7.949,col="red")
+abline(v = 7.949,col="red")
+axis(3,at=7.949,"7.949 MeV")
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="red")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="red")
+axis(3,at=7.688,"7.688 MeV")
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="red")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="red")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(50,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=3)
+# Rutherford Overlay
+plot(data2,type='l',xlim=c(50,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(50,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=3)
+plot(data2,type='l',xlim=c(50,205))
+plot(data2,type='line',xlim=c(50,205))
+plot(data2,type=l,xlim=c(50,205))
+plot(data2,type="l",xlim=c(50,205))
 ?plot
-plot(data1,type='c')
+plot(data2,type="l",xlim=c(50,205))
-?plot
+plot(data2,type="l",xlim=c(50,205))
-plot(data1,type='l')
-lines(data2)
-lines(data2,col='red')
-plot(data1,type='l',xlim=c(190,210))
-lines(data2,col='red')
-plot(data1,type='l',xlim=c(195,205))
-lines(data2,col='red')
-plot(data1,type='l',xlim=c(95,205))
-lines(data2,col='red')
 data2
-ls()
+q
-test1=c(1)
+plot(count~channel,data=data2,type='l',xlim=c(50,205))
-ls()
+lines(c(0,1023),c(7600,7600),col="blue")
-rm(test1)
+lines(count~channel,data=data3,col='red')
-ls()
+lines(c(0,1023),c(18500,18500),col="purple")
-max_cu_ruth = 17200
+minor.tick(nx=5,ny=2)
-lines
+dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=3)
-?lines
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
-lines(c(0,1023),c(17200,17200),col="blue")
+abline(v = 7.949,col="red")
-lines(c(0,1023),c(17400,17400),col="blue")
+axis(3,at=7.949,"7.949 MeV")
-lines(c(0,1023),c(17600,17600),col="blue")
+abline(v = 7.688,col="red")
-lines(c(0,1023),c(17500,17500),col="blue")
+axis(3,at=7.688,"7.688 MeV")
-plot(data1,type='l',xlim=c(95,205))
+minor.tick(nx=5,ny=2)
-lines(c(0,1023),c(17500,17500),col="blue")
+dev.print(pdf,"../report/nuclear.pdf",width=4.5,height=3)
-plot(data1,type='l',xlim=c(95,205))
+# Rutherford Overlay
-lines(c(0,1023),c(17600,17600),col="blue")
+plot(count~channel,data=data2,type='l',xlim=c(50,205))
-lines(data2,col='red')
+lines(c(0,1023),c(7600,7600),col="blue")
-lines(c(0,1023),c(20000,20000),col="green")
+lines(count~channel,data=data3,col='red')
-lines(c(0,1023),c(20000,20000),col="purple")
+lines(c(0,1023),c(18500,18500),col="purple")
-.2*20000
+minor.tick(nx=5,ny=2)
-?lines
+dev.print(pdf,"../report/rutherford.pdf",width=6,height=3)
-?plot
+# calibration close-up
-lines(c(0,1023),c(4000,4000),col="purple")
+plot(data2,type='l',xlim=c(185,205))
-.2*17600
+lines(c(0,1023),c(7600,7600),col="blue")
-lines(c(0,1023),c(3520,3520),col="blue")
+abline(h = 1520,col="blue",lwd=1)
-grid.locator
+abline(v = 189.12,col="blue",lwd=1)
-identify
+axis(1,at=189.12,padj=1.5,"189.12±0.6")
-identify(x,y)
+axis(3,at=189.12,"1.706±0.05 MeV")
-identify(200,16000)
+lines(data3,col='red')
-identify(length,coverage)
+lines(c(0,1023),c(18500,18500),col="pudatarple")
-identify(channel,count)
+abline(h = 3700,col="purple",lwd=1)
-identify("channel","count")
+abline(v = 203.63,col="purple",lwd=1)
-identify(channel,count)
+axis(1,at=203.63,padj=1.5,"203.63±0.6")
-identify(data1$channel,count)
+axis(3,at=203.63,"1.838±0.05 MeV")
-identify(data1$channel,data1$count)
+minor.tick(nx=5,ny=2)
-plot(data1,type='l',xlim=c(95,205))
+dev.print(pdf,"../report/calibration.pdf",width=6,height=3)
-lines(c(0,1023),c(17600,17600),col="blue")
+# nuclear reactions
-lines(c(0,1023),c(3520,3520),col="blue")
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
-plot(data1,type='l',xlim=c(95,205))
+abline(v = 7.949,col="red")
-lines(c(0,1023),c(17600,17600),col="blue")
+axis(3,at=7.949,"7.949 MeV")
-lines(data2,col='red')
+abline(v = 7.688,col="red")
-lines(c(0,1023),c(20000,20000),col="purple")
+axis(3,at=7.688,"7.688 MeV")
-dev.print(pdf,"../report/rutherford.pdf")
+minor.tick(nx=5,ny=2)
-?dev.print
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
-dev.print(pdf,"../report/rutherford.pdf"width=6,height=6)
+plot(data2,type='l',xlim=c(185,205))
-dev.print(pdf,"../report/rutherford.pdf",width=6,height=6)
+lines(c(0,1023),c(7600,7600),col="blue")
-clear
+abline(h = 1520,col="blue",lwd=1)
-clear()
+abline(v = 189.12,col="blue",lwd=1)
-dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=6)
+axis(1,at=189.12,padj=1.5,"189.12±0.6")
-dev.print(pdf,"../report/rutherford.pdf",width=4.5,height=6)
+axis(3,at=189.12,"1.706±0.05 MeV")
+lines(data3,col='red')
+lines(c(0,1023),c(18500,18500),col="pudatarple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.5,"203.63±0.6")
+axis(3,at=203.63,"1.838±0.05 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=6,height=3)
+plot(count~channel,data=data2,type='l',xlim=c(185,205))
+lines(c(0,1023),c(7600,7600),col="blue")
+abline(h = 1520,col="blue",lwd=1)
+abline(v = 189.12,col="blue",lwd=1)
+axis(1,at=189.12,padj=1.5,"189.12±0.6")
+axis(3,at=189.12,"1.706±0.05 MeV")
+lines(count~channel,data=data3,col='red')
+lines(c(0,1023),c(18500,18500),col="purple")
+abline(h = 3700,col="purple",lwd=1)
+abline(v = 203.63,col="purple",lwd=1)
+axis(1,at=203.63,padj=1.5,"203.63±0.6")
+axis(3,at=203.63,"1.838±0.05 MeV")
+minor.tick(nx=5,ny=2)
+dev.print(pdf,"../report/calibration.pdf",width=6,height=3)
+data1[7.8-7.9]
+data1[energy=7.8-7.9]
+data1[energy>7.8]
+data1[$energy>7.8]
+data1[data1$energy>7.8]
+plot(count~channel,data1)
+plot(count~channel,data1,xlim=c(840,870)))
+plot(count~channel,data1,xlim=c(840,870))
+plot(count~channel,data1,xlim=c(840,870),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(800,870),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(750,870),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(700,870),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(700,970),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(7800,850),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(780,850),ylim=c(0,100))
+plot(count~channel,data1,xlim=c(780,850),ylim=c(0,100),type=l)
+plot(count~channel,data1,xlim=c(780,850),ylim=c(0,100),type='l')
+plot(count~channel,data1,xlim=c(780,850),ylim=c(0,100),pch='|')
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="red")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="red")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=6,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="red")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="red")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~channel,data1,xlim=c(780,850),ylim=c(0,100),pch='|')
+data1
+peak1_interval = c(793,800)
+peak2_interval = c(838,847)
+interval
+seq
+seq(peak2_interval)
+seq(838,847(
+seq(838,847)
+peak2 = seq(838,847)
+peak1 = seq(793,800)
+peak1
+data1[peak1]
+data1[index==peak1]
+?subset
+data1[,peak1]
+data1[1,peak1]
+data1[1,]
+data1[,]
+data1[,1]
+data1[,peak1]
+data1[,index]
+data1[,$index]
+data1[,2]
+data1[,1]
+data1[,1==peak1]
+sum
+?sum
+data1[$count]
+data1[count]
+data1["count"]
+data1["count"][peak1]
+data1["count",peak1
+data1["count",peak1]
+data1["count"]
+peak1
+data1
+names(data1)
+data1["v1"]
+data1["channel"]
+data1["channel","count"]
+data1["channel":"count",]
+data1["channel":"count"]
+data1["channel","count"]
+data1["channel"]
+data1[c("channel","count")]
+data1[5:10]
+5:10
+data1[c(5:10)]
+data1[,c(5:10)]
+data1[c(5:10),]
+data1[peak1,]
+data1[peak2,]
+data1[0,]
+data1[1,]
+data1[801,]
+data1[802,]
+data1[801,]
+peak1
+peak1=793:801
+data1[801,]
+data1[peak1,]
+peak1=793:802
+data1[peak1,]
+data1[peak2,]
+peak2=837:849
+data1[peak2,]
+peak2=837:850
+data1[peak2,]
+peak2=836:850
+data1[peak2,]
+peak2=835:850
+data1[peak2,]
+peak2=834:850
+data1[peak2,]
+peak2=833:850
+data1[peak2,]
+?sum
+data1[peak2,"energy"]
+data1[peak2,"count"]
+sum(data1[peak2,"count"])
+sum(data1[peak1,"count"])
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="red")
+abline(v = 7.7,col="blue")
+abline(v = 6.9,col="blue")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="red")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+7.949-6.9
+1.049/6.9
+7.688-7.7
+0.012/7.7
+sum(data1[peak1,"count"])
+sum(data1[peak2,"count"])
+3.12/3
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+abline(v = 7.588,col="purple")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+abline(v = 7.58,col="purple")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+abline(v = 7.583,col="purple")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+axis(3,at=7.175,"7.175 MeV")
+abline(v = 7.583,col="purple")
+axis(3,at=7.583,"7.583 MeV")
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+axis(3,at=7.175,"7.175 MeV",padj=1)
+abline(v = 7.583,col="purple")
+axis(3,at=7.583,"7.583 MeV",padj=1)
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+axis(3,at=7.175,"7.175 MeV",padj=1.2)
+abline(v = 7.583,col="purple")
+axis(3,at=7.583,"7.583 MeV",padj=1.2)
+axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+axis(3,at=7.175,"7.175 MeV",padj=1.2)
+abline(v = 7.583,col="purple")
+axis(3,at=7.583,"7.583 MeV",padj=1.2)
+axis(3,at=7.949,"7.949 MeV",padj=-.3)
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688 MeV",padj=-.3)
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100),xlab="energy (MeV)")
+abline(v = 7.949,col="blue")
+abline(v = 7.175,col="purple")
+axis(3,at=7.175,"7.175")
+abline(v = 7.583,col="purple")
+axis(3,at=7.583,"7.583")
+axis(3,at=7.949,"7.949")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(0.5,2.5),ylim=c(0,100),xlab="energy (MeV)")
+minor.tick(nx=8,ny=2)
+plot(count~energy,data=data1,type='l',xlim=c(0.5,2.5),ylim=c(0,20000),xlab="energy (MeV)")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/thickness.pdf",width=6,height=3)
+plot(count~energy,data=data1,type='l',xlim=c(0.5,2.5),ylim=c(0,25000),xlab="energy (MeV)")
+minor.tick(nx=8,ny=2)
+dev.print(pdf,"../report/thickness.pdf",width=6,height=3)
 quit()

accelerator/data/plots.R

@@ -26,19 +26,23 @@ minor.tick(nx=5,ny=2)
 dev.print(pdf,"../report/calibration.pdf",width=6,height=3)
 
 # nuclear reactions
-plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100))
+plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100),xlab="energy (MeV)")
-abline(v = 7.949,col="red")
+abline(v = 7.949,col="blue")
-axis(3,at=7.949,"7.949 MeV")
+abline(v = 7.175,col="purple")
-abline(v = 7.688,col="red")
+axis(3,at=7.175,"7.175")
-axis(3,at=7.688,"7.688 MeV")
+abline(v = 7.583,col="purple")
-minor.tick(nx=5,ny=2)
+axis(3,at=7.583,"7.583")
+axis(3,at=7.949,"7.949")
+abline(v = 7.688,col="blue")
+axis(3,at=7.688,"7.688")
+minor.tick(nx=8,ny=2)
 dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)
 
 
-lines(c(0,1023),c(7600,7600),col="blue")
+#
-lines(data3,col='red')
+plot(count~energy,data=data1,type='l',xlim=c(0.5,2.5),ylim=c(0,25000),xlab="energy (MeV)")
-lines(c(0,1023),c(18500,18500),col="purple")
+minor.tick(nx=8,ny=2)
-
+dev.print(pdf,"../report/thickness.pdf",width=6,height=3)
 
 
 

accelerator/report/report.tex

@@ -33,7 +33,7 @@
 \maketitle
 
 \begin{abstract}
-A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF foil. Alpha particle detection is used to verify the nuclear reactions involved. The probabilty cross-sections are computed for the nuclear reactions \FpaO\ and \LipaHe.
+A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF foil, transforming them to helium and oxygen through the nuclear reactions \FpaO\ and \LipaHe. Alpha particle detection is used to verify the nuclear reactions involved. Rutherford scattering of a proton against silicon and copper atoms is used to calibrate a kinetic energy scale to the channels of the MCA, but some problems with this are indicated by an imprecise fitting to the nuclear reaction peaks. The nuclear reaction peaks are nonetheless identified and their differential cross-section ratios are computed and compared positively with known values. Absolute cross-sections are also computed, but are dubious due to an unknown foil thickness.
 \end{abstract}
 
 %─────────────
@@ -41,7 +41,7 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
     \label{sec:intro}
     The nuclear properties of lithium are of interest, especially the reaction differential cross-section for \LipaHe. Studies of the Sun's photosphere show the abundance of lithium relative to hydrogen and helium less nearly an order of magnitude. A large cross-section for \LipaHe\ is believed responsible; it predicts that ionized hydrogen will readily collide with lithium, transforming the lithium to helium, and emitting an alpha particle. This is one transition that takes place in stellar nucleosynthesis, and is maintained as fresh lithium is carried toward a star's core by convective currents, but even with this process and reaction in mind, modern astrophysicists have yet to completely explain the lack of abundant lithium in our sun's photosphere. Studies of the nuclear properties of lithium could elucidate a better stellar structure model, but this is outside the scope of our study. \cite{Carroll&Ostlie}
 
-    Fluorine can be rearranged in a similar fashion. It is one of the rarest elements observed by astronomers, and thought to be for the same reasons: it is readily rearranged by a proton to produce oxygen and an alpha particle. Figure~\ref{fig:abundances} shows relative abundances of many elements. To judge whether the high-probability explanation is plausible, we will determine the reaction differential cross-sections of the fluorine-proton reaction \FpaO\ and the lithium-proton reaction \LipaHe. In this study, we performed a prompt radiation analysis by observing the alpha particle products of each reaction, and from the kinetic energy spectrum of these products, the differential cross-sections can be computed.\\
+    Fluorine can be rearranged in a similar fashion. It is one of the rarest elements observed by astronomers, and thought to be for the same reasons: it is readily rearranged by a proton to produce oxygen and an alpha particle. Figure~\ref{fig:abundances} shows relative abundances of many elements. To judge whether the high-probability explanation is plausible, we will determine the reaction differential cross-sections of the fluorine-proton reaction \FpaO\ and the lithium-proton reaction \LipaHe. In this study, we performed a prompt radiation analysis by observing the alpha particle products of each reaction, and from the kinetic energy spectrum of these products, the differential cross-sections are computed.\\
 
     \begin{figure}
         \center
@@ -57,7 +57,7 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
 
 \section{Proton Beam and Detector}
     \label{sec:detector}
-    The Tandem Van de Graff Accelerator Lab provided a $1.95\pm0.05$ MeV proton beam for three experiments. When incident on a lithium-fluoride foil, we expect the nuclear reactions described in Section~\ref{sec:reactions} to occur. When the beam is incident on a silicon or copper foil, we expect Rutherford scattering. We used a circular normal-faced surface barrier detector to observe the alpha particle products of \FpaO\ and \LipaHe\ and the protons from Rutherford scattering. \cite{ADVLABACCEL} The detector was positioned at $149.95\degree\pm0.05\degree$ from the proton beam, which we define as the lab frame of reference; see figure~\ref{fig:detector}. The detector covers a solid angle $\Omega = 1.895\pm0.001$ steradians. In each experiment, the beam is run until total integrated charged reaches $2\times10^{-4}$ coulombs. 
+    The Tandem Van de Graff Accelerator Lab provided a $1.95\pm0.05$ MeV proton beam for three experiments. When incident on a lithium-fluoride foil, we expect the nuclear reactions described in Section~\ref{sec:reactions} to occur. When the beam is incident on a silicon or copper foil, we expect Rutherford scattering. We used a circular normal-faced surface barrier detector to observe the alpha particle products of \FpaO\ and \LipaHe\ and the protons from Rutherford scattering. \cite{ADVLABACCEL} The detector was positioned at $149.95\degree\pm0.05\degree$ from the proton beam, which we define as the lab frame of reference; see figure~\ref{fig:detector}. The detector covers a solid angle $\Omega = 1.895\pm0.001$ steradians. In each experiment, the beam is run until total integrated charged reaches $2.00000\times10^{-4}$ coulombs, corresponding to a total number of incident beam particles n = 1.24830$\times$10$^{15}$ protons. 
 
     \begin{figure}
         \center
@@ -138,8 +138,9 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
 
         \begin{table}
             \center
-            \begin{tabular}{rl}
+            \begin{tabular}{rlll}
-                Reaction&Energy (MeV) \\
+                Reaction&Energy (MeV)&\\
+                &Computed&Pub.&Dev. \\
                 \hline
                 % From Kayani's(?) kinematic factors
                 %$^{28}$Si(p)&0.352$\pm$0.009\\
@@ -148,25 +149,25 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
                 $^{28}$Si(p)&1.706$\pm$0.05\\
                 $^{63}$Cu(p)&1.837$\pm$0.05\\
                 $^{65}$Cu(p)&1.840$\pm$0.05\\
-                \FpaO&7.949\pm0.03\\
+                \FpaO&7.949$\pm$0.03&6.9&1.049(15\%)\\
-                \LipaHe&7.688\pm0.03\\
+                \LipaHe&7.688$\pm$0.03&7.7&0.012(0.2\%)\\
 
             \end{tabular}
-            \caption{Expected peaks for nuclear reactions and maximum energy of a Rutherford scattered proton. Rutherford scattering energies are computed using equation~\ref{eq:rutherford} with the kinematic factors from table~\ref{tab:nuclei}.}
+            \caption{Expected kinetic energies for nuclear reactions and maximum energy of a Rutherford scattered proton. Rutherford scattering energies are computed using equation~\ref{eq:rutherford} with the kinematic factors from table~\ref{tab:nuclei}. The expected alpha particle energy for \LipaHe\ is in good agreement with that published in Chu et al., but the expectation for \FpaO\ deviates by 15\%. \cite{Chuetal}}
             \label{tab:predictions}
         \end{table}
 
 
     \subsection{Nuclear Reaction Peaks}
     \label{sec:reactions:peaks}
-        The kinetic energy of the alpha particle products from \FpaO and \LipaHe are characteristic of those reactions. Binding energies of the involved nuclei are significant compared to their rest masses, so the relativistic equivalence must be considered when computing the energy Q released or absorbed during the reaction, \cite{ADVLABACCEL} so
+        The kinetic energy of the alpha particle products from \FpaO\ and \LipaHe\ are characteristic of those reactions. Binding energies of the involved nuclei are significant compared to their rest masses, so the relativistic equivalence must be considered when computing the energy Q released or absorbed during the reaction, \cite{ADVLABACCEL} so
 
         \begin{equation}
              Q = \delta(mc^2) = (M1+M2)c^2 - (M3+M4)c^2.
              \label{eq:Q}
          \end{equation}
 
-        Given this method of computing Q, non-relativistic conservation of total energy and momentum provide a sufficiently useful expression for the kinetic energy of the alpha particle product E3 as a function of the kinematic quantities described in figure~\ref{fig:kinematics}. \cite{Ziegler_1975} With results in table~\ref{tab:predictions}, the expectation values of E3 were computed as
+        After computing Q this way, non-relativistic conservations of total energy and momentum provide a sufficiently useful expression for the kinetic energy of the alpha particle product E3 as a function of the kinematic quantities described in figure~\ref{fig:kinematics}. \cite{Ziegler_1975} With results in table~\ref{tab:predictions}, the expectation values of E3 were computed as \cite{Meisel1996}
 
         \begin{equation}
             E3^{1/2} = A\pm(A^2+B)^{1/2}, 
@@ -175,7 +176,7 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
             A = [(M1{\times}M3{\times}E1)^{1/2}/(M3+M4)]cos\theta
         \end{equation} and
         \begin{equation}
-            B = [M4{\times}Q+E1(M4-M1)]/(M3+M4). \cite{Meisel1996}
+            B = [M4{\times}Q+E1(M4-M1)]/(M3+M4). 
         \end{equation}
 
         %\begin{equation}
@@ -191,14 +192,12 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
 \section{Results}
     \label{sec:results}
 
-        The Rutherford scattering curves used to calibrate the energy scale are shown in figures \ref{fig:rutherford} and /ref{fig:calibration}. The best fit for this linear scale is 
+        The Rutherford scattering curves used to calibrate the energy scale are shown in figures \ref{fig:rutherford} and \ref{fig:calibration}. The best fit for this linear scale is 
         \begin{equation}
             x = 0.009\ \textrm{MeV}\times\textrm{channel}+0.00392\ \textrm{MeV}.
             \label{eq:scale}
         \end{equation}
 
-        An attempt is made to locate the predicted peaks, and instead two peaks are found at .
-
         \begin{figure}
             \center
             \includegraphics[width=6in]{rutherford.pdf}
@@ -213,21 +212,73 @@ A 2 MeV proton beam is used to annihilate lithium and flourine atoms from a LiF
             \label{fig:calibration}
         \end{figure}
 
+        An attempt is made to locate the predicted peaks for the alpha particle products of \LipaHe\ and \FpaO\ in figure~\ref{fig:peaks}. Two peaks are visible, but not at the predicted energies under our calibration. Presuming our calibration is off, the counts under these peaks are integrated to be used in computing the differential cross-section.
+
         \begin{figure}
             \center
             \includegraphics[width=6in]{nuclear.pdf}
-            \caption{Two peaks were observed not far from the predicted energies along the calibrated scale. The peaks do not match the expected values, but we progress under the assumption that the scale is wrong and these are in fact the alpha particles predicted as products of the \LipaHe and \FpaO reactions.}
+            \caption{Two peaks were observed not far from the predicted energies along the calibrated scale. The peaks do not match the computed expected values (blue), but we progress under the assumption that the scale is wrong and the peaks identified (purple) are in fact the alpha particles predicted as products of the \LipaHe\ and \FpaO\ reactions.}
             \label{fig:peaks}
         \end{figure}
 
+        \subsection{Yield and Differential Cross-Sections}
+            \label{sec:results:cross-sections}
+
+            We observed the reaction yield Y($\theta$) as the total count integrated under the curve for each reaction. Computing the differential cross-section for a reaction is done using \cite{Ziegler_1975}
+            \begin{equation}
+                \sigma(\theta,E) = Y(\theta,E)/(n N \delta x \Omega),
+                \label{eq:crosssection}
+            \end{equation} 
+            where \\
+            \begin{tabular}[h!]{llll}
+                ~~~~~~~~~~~~~~~~~~~~~&$\theta$&=&detector angle,\\
+                ~~~~~~~~~~~~~~~~~~~~~&E&=&energy referring to a specific reaction,\\
+                ~~~~~~~~~~~~~~~~~~~~~&n&=&number of incident beam particles,\\
+                ~~~~~~~~~~~~~~~~~~~~~&N&=&volume number density of target atoms,\\
+                ~~~~~~~~~~~~~~~~~~~~~&$\delta$x&=&target thickness,\\
+                ~~~~~~~~~~~~~~~~~~~~~&$\Omega$&=&detector solid angle.\\                
+            \end{tabular}
+
+
+            Beam and detector parameters can be referenced from section~\ref{sec:detector}. The number densities for Li and F in an LiF foil are N(Li) = N(F) = 6.16 $\times$10$^{22}$ atoms/cm$^3$. \cite{ashcroft1976solid} However, the foil thickness is not known. Our best guess is 200$\pm$20 \AA, but not knowing this thickness may dictate we only compute the ratio of the cross-sections rather than their absolute values. From equation \ref{eq:crosssection},
+            \begin{equation}
+                \frac{\sigma(E_1)}{\sigma(E_2)} = \frac{Y(E_1)}{Y(E_2)}.
+                \label{eq:ratios}
+            \end{equation}
+
+            \begin{table}
+                \center
+                \begin{tabular}{rllrr}
+                    Reaction&Yield&Ratio&$\sigma$ (cm$^2$)&$\sigma$ (barns)\\
+                    \hline
+                    \LipaHe&428&3.12&(1.48$\pm$0.15)$\times$10$^{-38}$&(1.48$\pm$0.15)$\times$10$^-14$     \\
+                    \FpaO&137&0.320&(0.475$\pm$0.047)$\times$10$^{-38}$&(0.475$\pm$0.047)$\times$10$^-14$\\
+
+                \end{tabular}
+                \caption{Yields and differential cross-sections computed for the reactions of interest. The ratio of each reaction's cross-section to the other is tabulated. The cross-section is computed using a foil thickness of 200$\pm$20\AA, but this is only a guess.}
+                \label{tab:results}
+            \end{table}
+
+        \subsection{Foil Thickness}
+            \label{sec:results:thickness}
+            The foil thickness $\delta x$ is not known a priori but it may be determined using the Rutherford scattering of the alpha particle product from \FpaO. The film thickness is less than 1000 \AA, so it can be computed using the surface energy approximation as \cite{Feldman1986}
+            \begin{equation}
+                \delta x = \delta E1 \{K [dE/dx]_{E1} + |cos\theta|^{-1} [dE/dx]_{KE1}\}^{-1}.
+            \end{equation}
+
+            Here, $\delta$ E1 is the full width at half maximum of the Rutherford-scattered peak given a film thickness $\delta$ x. The stopping power terms [dE/dx] are referenced from appendix F of Chu et al., \cite{Chuetal} where E1 refers to the incident alpha particle (the product of the \FpaO\ reaction), and KE1 refers to the Rutherford-scattered alpha particle. The table of stopping cross sections consulted \cite{Chuetal} did not provide values for the known alpha particle energy from this reaction, so an attempt was made to compute the value using the polynomial fit provided in table VII of that text. The output from this attempt was nonsense, so while this is a viable method for computing the foil thickness, thus allowing a better computation of the differential cross-sections of both reactions, the task of computing the foil thickness is not completed here.
+            
+
 %─────────────
 \section{Conclusion}
     \label{sec:conclusion}
 
-    The energy scale may be off due to a poor choice in locating the Rutherford scattering energy along the curve, however, look at the different between selecting the 100\% mark over the 20\% reveals a change in the scale of only about .018 MeV, less than 10\% of the scale's deviation from the observed nuclear reaction peaks. This indicates a more significant flaw in the analysis remains to be discovered. 
+    The energy scale may be mis-calibrated due to a poor choice in locating the Rutherford scattering energy along the curve, however, looking at the difference between selecting the 100\% mark rather than the 20\% reveals a scale shift of only ~.018 MeV, less than 10\% of the scale's deviation from the observed nuclear reaction peaks. This indicates a more significant flaw in the analysis remains to be uncovered. However, the peaks in the kinetic energy spectrum related to \FpaO\ and \LipaHe\ were identified near 7.175 MeV and 7.583 MeV respectively, and counts were taken by integrating under those features.
 
+    The ratio of the counts was used to compute the ratio of the differential cross-sections between these reactions, as in equation~\ref{eq:ratios}. For \FpaO\ relative to \LipaHe\, the ratio is 0.320. Chu et al. report yields for \FpaO\ and \LipaHe\ at 3 counts/$\mu$C and 9 counts/$\mu$C respectively \cite{Chuetal}, giving a ratio of 1/3. Our result deviates by 4\%, indicating a strong agreement with published values.
+
+    Absolute values for the differential cross-sections of each reaction are computed in cm$^{2}$ and in barns, but these rely on a guess for the LiF foil thickness. An attempt was made to compute the foil thickness, but it ended in no useful values. With further work, this computation may be possible using only the information contained in this study. Without a value, the absolute differential cross-sections have little meaning, and can't inform the availability of these processes for stellar nuclear processes. However, it is clear that there is at least some significant availability, which could be sufficient in the proton-rich environment of stellar plasmas.
 
 \printbibliography
 
-
 \end{document}

adv_lab.bib

@@ -51,6 +51,28 @@ url = {http://www.panalytical.com/Empyrean.htm}
 
 
 
+
+@book{Feldman1986,
+  title={Fundamentals of Surface Thin Film Analysis},
+  author={Feldman, Leonard C.},
+  isbn={9780135005705},
+  publisher={Prentice Hall PTR},
+  year={1986},
+  month=aug
+}
+
+
+@book{ashcroft1976solid,
+  title={Solid state physics},
+  author={Ashcroft, N.W. and Mermin, N.D.},
+  isbn={9780030493461},
+  lccn={lc74009772},
+  series={Science: Physics},
+  url={https://books.google.com/books?id=FRZRAAAAMAAJ},
+  year={1976},
+  publisher={Saunders College}
+}
+
 @Inbook{Meisel1996,
 author="Meisel, W.",
 editor="Long, Gary J.