%% Electron Diffraction
close all; clear all; clc

%constants
L=.130;
m=9.11*10^-31;
e=1.6*10^-19;
h=6.626*10^-34;

%Gathered Data:
V=[(4900:-100:3600),3400,3200];
%OD=[38.62324,39.76624,40.3098,40.89400,41.66794,...
%    41.66794,42.38752,43.7388,43.36288,45.31106,...
%    45.62094,45.6438,47.7393,48.38700,50.01006,...
%    52.83454];
OD=[36.99,37.11,37.31,37.63,38.02,38.28,38.64,39.06,...
    39.45,39.86,40.15,40.55,40.92,41.19,41.87,42.23]
dOD=[1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,...
    1.7,1.7,1.7,1.7,1.7];%this is error in OD

OD=OD*10^-3;
dOD=dOD*10^-3;

ID=[20.35,20.35,21.74,22.04,22.50,22.86,22.24,22.97,23.03,...
    23.23,23.55,23.74,24.17,24.41,24.78,25.04];

%ID=[24.1555,24.38400,24.4792,24.58212,25.1206,...
%    25.89022,28.70200,28.88234,29.45384,29.7307,...
%    30.1498,30.23616,31.0515,31.87700,32.2072,...
%    32.4739]; this is the first and unsuccesful run
dID=[1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,...
    1.7,1.7,1.7,1.7,1.7];

ID=ID*10^-3;
dID=dID*10^-3;

%% optical corrections for length
R=66*10^-3;
DL1=R*(1-cos(asin(OD/(2*R))));%correction for length
DT1=1.5*10^-3*sin(atan(OD/(2*(L+DL1))));%correction for thickness
DL2=R*(1-cos(asin(ID/(2*R))));
DT2=1.5*10^-3*sin(atan(ID/(2*(L+DL2))));
L1=L-DT1-DL1;
L2=L-DT2-DL2;

%% outer diameter lsr fit
clc
figure
ODactual=.123;
%least squares fit
lsrvec=min(1./sqrt(V)):10e-6:max(1./sqrt(V));
p = polyfit(1./sqrt(V),OD,1);

p(1)=2.510;p(2)=0;

lsr=polyval(p,lsrvec);
plot(1./sqrt(V),OD,'x',lsrvec,lsr);
hold on; errorbar(1./sqrt(V),OD,dOD,'x');hold off
xlabel('1/sqrt(V)');ylabel('Outer Diameter')
set(gcf,'color',[1,1,1])
legend('Data','Least Squares Line');
OuterSlope=p(1);

odcalc=2.*mean(L1).*h/(sqrt(2*m*e)*OuterSlope*10^-9)%decided to use the mean

Error=100*(ODactual-odcalc)/ODactual

%% inner diameter lsr fit
figure
IDactual=.213;
%least squares fit
lsrvec=min(1./sqrt(V)):10e-6:max(1./sqrt(V));
p = polyfit(1./sqrt(V),ID,1);
p(1)=1.465;p(2)=0;
lsr=polyval(p,lsrvec);
plot(1./sqrt(V),ID,'x',lsrvec,lsr);set(gcf,'color',[1,1,1]);
hold on; errorbar(1./sqrt(V),ID,dID,'x'); hold off
xlabel('1/sqrt(V)');ylabel('Outer Diameter')
legend('Data','Least Squares Line');
InnerSlope=p(1);

idcalc=2*mean(L2)*h/(sqrt(2*m*e)*InnerSlope)/10^-9
Error=100*(IDactual-idcalc)/IDactual

%% All data plot
close all
ActualVec=linspace(min(V),max(V),100);

%One spacing
D1=2*h*L2./(ID.*sqrt(2*m*e).*sqrt(V)*10^-9)
IDErrBars=D1.*dID./ID;
figure
plot(V,D1,'x',ActualVec,IDactual*ones(size(ActualVec)));set(gcf,'color',[1,1,1]);
hold on
errorbar(V,D1,IDErrBars,'x')
xlabel('Voltage (V)');ylabel('Lattice Spacing(nm)');
%ploting mean and sem
plot(V,mean(D1)*ones(size(V)),'r')
plot(V,(mean(D1)+std(D1)./sqrt(length(D1))).*ones(size(V)),'g',...
    V,(mean(D1)-std(D1)./sqrt(length(D1))).*ones(size(V)),'g')
hold off
legend('measured','actual','ebars','mean','sem')
%means
%PError1=100*(IDactual-mean(D1))/IDactual

%Second Spacing
D2=2*h*L1./(OD.*sqrt(2*m*e).*sqrt(V)*10^-9);
ODErrBars=D2.*dOD./OD;
figure
plot(V,D2,'x',ActualVec,ODactual*ones(size(ActualVec)));set(gcf,'color',[1,1,1])
hold on
errorbar(V,D2,ODErrBars,'x')
xlabel('Voltage (V)');ylabel('Lattice Spacing(nm)');
%ploting mean and sem
plot(V,mean(D2)*ones(size(V)),'r')
plot(V,(mean(D2)+std(D2)./sqrt(length(D2))).*ones(size(V)),'g',...
    V,(mean(D2)-std(D2)./sqrt(length(D2))).*ones(size(V)),'g')
hold off
legend('measured','actual','ebars','mean','sem')
%means

%% Means and SEMS
MeanD1=mean(D1)
MeanD2=mean(D2)

Sem1=std(D1)/sqrt(length(D1))
Sem2=std(D2)/sqrt(length(D2))

PError1=100*(IDactual-mean(D1))/IDactual
PError2=100*(ODactual-mean(D2))/ODactual