From d2bf32953fafb04fcf463b30361ad31394fe2a3d Mon Sep 17 00:00:00 2001
From: Peter DeRosa <54421997+MagnusSnowleopard@users.noreply.github.com>
Date: Mon, 22 Aug 2022 12:05:21 -0400
Subject: [PATCH] General documentation update

---
 .AD.cxx.swo | Bin 16384 -> 0 bytes
 326.csv     |  15 +++++++++++++
 426.csv     |  14 +++++++++++++
 AD.cxx      |  59 +++++++++++++++++++++++++++++-----------------------
 Cleb.h      |  10 +++++++--
 Functlib.h  |  34 ++++++++++++++++++------------
 GUI_AD.h    |  30 +++++++++++++++-----------
 GUI_Base.h  |  14 +++++++------
 QDK.h       |   8 +++++++
 ad.txt      |   8 +++----
 global.h    |   8 ++++---
 11 files changed, 134 insertions(+), 66 deletions(-)
 delete mode 100644 .AD.cxx.swo
 create mode 100644 326.csv
 create mode 100644 426.csv

diff --git a/.AD.cxx.swo b/.AD.cxx.swo
deleted file mode 100644
index 20bea15f9d5db3bdb454203b88f9c29efba99197..0000000000000000000000000000000000000000
GIT binary patch
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HcmV?d00001

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diff --git a/326.csv b/326.csv
new file mode 100644
index 0000000..cdc5759
--- /dev/null
+++ b/326.csv
@@ -0,0 +1,15 @@
+x, y, y_err
+50.24390, 1.01725,0.04
+58.536584, 1.01478,0.04
+69.26829, 1.07394,0.04
+79.02439, 1.15528,0.04
+80.48780, 1.08380,0.04
+89.75609, 1.11584,0.04
+98.53658, 1.02957,0.04
+100.48788, 1.05176,0.04
+110.2439, 1.04436,0.04
+121.46345, 1.01725,0.04
+129.7560, 1.00985,0.04
+141.9512, 0.8693,0.04
+147.3170, 0.90633,0.04
+161.9512, 0.78309,0.04
diff --git a/426.csv b/426.csv
new file mode 100644
index 0000000..0718e00
--- /dev/null
+++ b/426.csv
@@ -0,0 +1,14 @@
+x, y, y_err
+50.73177, 1.06408,0.04
+58.536554, 0.99757,0.04
+70.2439, 0.896478,0.04
+79.51211, 0.84471,0.04
+80.48788, 0.81267,0.04
+89.7560, 0.891549,0.04
+100.48778, 0.93839,0.04
+98.53655, 0.86197,0.04
+109.7566, 0.90387,0.04
+121.46335, 0.97046,0.04
+141.9511, 1.11338,0.04
+147.8045, 1.15774,0.04
+161.9511, 1.25880,0.04
diff --git a/AD.cxx b/AD.cxx
index c541247..3b9c2a0 100644
--- a/AD.cxx
+++ b/AD.cxx
@@ -1,3 +1,26 @@
+//#################################################################
+//  This program is the main functional of an Angular Ditribution 
+//  calculation to fit and determine accepted values of delta.
+//
+//  Input file need is two .csv, one is a table of racah values, 
+//  the second is the experimental data file. The program can handle
+//  any amount of angles of detectors.  
+//
+//  The inputs needed are j1 and j2 values, the gamma-ray  ,the radius, 
+//  distance and depth of the detectors, and the sigma of magnetic 
+//  substate distribution following the reaction of interest. 
+//
+//  The program generates 2 graphs - 1 Visible Angular distribution
+//  plot and fit normalized by A0. - 2 The log(Chi-squared) vs 
+//  arctan(delta) graph. 
+//
+//  The program also outputs a ad.txt which has QDK coeff. and other
+//  detector parameters.  
+//
+//To compile : g++ AD.cxx -o {Input Executable Name} -lX11
+//For more information about angular distributions, read Rose and Brinks, and Frank Moore (1988). 
+//#################################################################
+
 #include "global.h"
 
 #include "GUI_AD.h"
@@ -7,9 +30,6 @@
 #include "Cleb.h"
 
 
-//To compile : g++ AD.cxx -o {Input Executable Name} -lX11
-//For more information about angular distributions, read Rose and Brinks, and Frank Moore (1988). 
-
 using namespace std;
 #ifndef __CINT__ 
 
@@ -38,12 +58,12 @@ int main(int argc,char **argv){
     targetdistance = 4.;
     detthickness = 5.;
 
-    Energy = 1147.;
-    Sigma = .5; 
+    Energy = 426.;
+    Sigma = 1.0; 
 
 
-    j1 = 5.5; 
-    j2 = 3.5;
+    j1 = 7.5; 
+    j2 = 5.5;
     //--------------------------------
 
     //TEST MODE? y : 1 || n = 0
@@ -204,30 +224,16 @@ int main(int argc,char **argv){
         double aa = dangle[i]; 
 
         dangler.push_back(aa*3.14159/180.);
-        printf("dangle = %lf\n",dangler[i]);
+        printf("Angle %d = %lf\n",i,dangler[i]);
     }
     
 
 
-    // if you need to scale the y data by sin(theta)	
-
-
-    /*
-       for(int i=0; i<content.size(); i++){
-       for(int j=0; j<content[i].size(); j++){
-       cout<< content[i][j]<<" ";
-       }
-       cout<<"\n";
-       }
-       */
     //legendre fitting 
     // F[xi] = A0(1) + A2(P2(cos(xi))) + A4(P4(cos(xi)))
     //xi data is angle data in radians. 
     //yi data is y-intensity data. 
 
-    //to change the number of angles, just mess with the indexing of the read in and arrays. 
-
-
     //12 constants. this will build our matrix for gaussian elinmination. 
     //[a1 a2   a3] [A0] = [a4]
     //[a5 a6   a7] [A2] = [a8]
@@ -323,8 +329,8 @@ int main(int argc,char **argv){
 
 
     cout<<"A0 = "<<residual[0]<<"\n";
-    cout<<"A2 = "<<residual[1]<<"\n";
-    cout<<"A4 = "<<residual[2]<<"\n";
+    cout<<"a2 = "<<residual[1]/residual[0]<<"\n";
+    cout<<"a4 = "<<residual[2]/residual[0]<<"\n";
 
 
 
@@ -779,7 +785,7 @@ int main(int argc,char **argv){
     for(int i = 0; i < dydata.size(); i++){
         double bbb = dydata[i]; 
 
-        dydatas.push_back(bbb/A0E);
+         dydatas.push_back(bbb/A0E);
         //  printf("Normalized y-intensity %i = %lf\n",i+1,dydatas[i]);
 
     }
@@ -845,7 +851,8 @@ int main(int argc,char **argv){
         }else if(optnum == 2 and param == 1){
 
             optnum = -1;
-            gui_ad.SetData(dangler,dydatas);
+           // gui_ad.SetData(dangler,dydata); //dydata means you  are using already normalizing data.
+            gui_ad.SetData(dangler,dydatas); //dydatas means you are using non-A0 normalized data to start with.
             gui_ad.SetErrors(deydata);
             gui_ad.SetFit(residual[0],residual[1],residual[2]);
 
diff --git a/Cleb.h b/Cleb.h
index 7dba0a7..b57e8b6 100644
--- a/Cleb.h
+++ b/Cleb.h
@@ -1,7 +1,13 @@
-
-#include "global.h"
+//#############################################################
 //To compile : g++ AD.cxx -o {Input Executable Name} -lX11
 //#include "Coeff.h"
+//
+//This file contains member functions of Clebsh-Gordan functions
+//and other methods to caluculate 3J and 6J symbols if needed
+//for direct Racah calculations. 
+//
+//#############################################################
+#include "global.h"
 
 using namespace std;
 
diff --git a/Functlib.h b/Functlib.h
index 75006d0..2fbb72f 100644
--- a/Functlib.h
+++ b/Functlib.h
@@ -1,6 +1,9 @@
-
+//################################################################
+// This file contains the menu outputs and also misc conversion 
+// functions used throughout the program.  
+//
+//################################################################
 #include "global.h"
-//To compile : g++ AD.cxx -o {Input Executable Name} -lX11
 
 using namespace std;
 
@@ -20,22 +23,27 @@ void menu(){
 
 void Readme(){
 
-	std::cout<< "                                          \n";
-	std::cout<< " The program calculates Chi-Squared values \n";
+	std::cout<< "                                            \n";
+	std::cout<< " The program calculates Chi-Squared values  \n";
 	std::cout<< " from experimental angular distributions as \n";
-	std::cout<< " a function of multipole ratios using the \n"; 
-	std::cout<< " theoretical angular distribution formulae \n"; 
-	std::cout<< " in rose and brink \n";
+	std::cout<< " a function of multipole ratios using the   \n"; 
+	std::cout<< " theoretical angular distribution formulae  \n"; 
+	std::cout<< " in Rose and Brinks.                        \n";
 	std::cout<< " \n"; 
 	std::cout<< " Follow the prompt in order to correctly display \n";
 	std::cout<< " \n";
-	std::cout<< " To close the gui, press most buttons. \n";
+	std::cout<< " To close the gui, press most buttons.      \n";
 	std::cout<< " To zoom in, left click then drag and let go. To unzoom\n";
-	std::cout<< " press the space bar. To draw, right click\n";
-	std::cout<< "                                          \n";
-	std::cout<< " ad.txt is generated with geometric stats.\n";
-	std::cout<< " Then at the end it generates CG/Racah\n";	
-	std::cout<< "                                          \n";
+	std::cout<< " press the space bar. To draw, right click. \n";
+	std::cout<< "                                            \n";
+	std::cout<< " ad.txt is generated with geometric stats.  \n";
+	std::cout<< " Multiple different vectors available for   \n";	
+	std::cout<< " other analysis perspectives.               \n";
+	std::cout<< "                                            \n";
+	std::cout<< " To run in test mode, see the top of AD.cxx.\n";
+	std::cout<< " Running in test mode allows for faster use.\n";	
+	std::cout<< "                                            \n";
+	std::cout<< "                                            \n";
 }
 
 int param_run(int dt, int gt, int at, int st, int jt){
diff --git a/GUI_AD.h b/GUI_AD.h
index c8e3ed1..aa832d5 100644
--- a/GUI_AD.h
+++ b/GUI_AD.h
@@ -1,10 +1,15 @@
-#include "global.h"
-
-//To compile : g++ AD.cxx -o {Input Executable Name} -lX11
+//#############################################################################
+//
 // VERSION : 1.1 (Overlay for Angular Fit Display) 
-// Created with thanks to Daniel Folds Holt - University of Cambridge Cavendish Lab
+//
+// The  purpose of this GUI is for displaying angular distributions of the 
+// gamma-ray decays inputed via the *.csv file. It is equipped with error 
+// bars and a fit overlay. The output of this file is scaled by A0. 
+//
+//############################################################################
 
 
+#include "global.h"
 
 
 using namespace std;
@@ -209,10 +214,11 @@ int HistoGUIad::Zoom(int mouse_x, int mouse_y){
 double HistoGUIad::legval(double theta){
 	
 	double lg;
-	
-	double	aaa = A0/A0; 
-	double 	aab  = (A2E/A0)*(1.5 * pow(cos(theta),2) - .5);
-    double  aac  = (A4E/A0)*(35./8. * pow(cos(theta),4) - 30./8. * pow(cos(theta),2)  +  3./8. );
+	double norm = A0; 
+
+	double	aaa = A0/norm; 
+	double 	aab  = (A2E/norm)*(1.5 * pow(cos(theta),2) - .5);
+    double  aac  = (A4E/norm)*(35./8. * pow(cos(theta),4) - 30./8. * pow(cos(theta),2)  +  3./8. );
 	
 	
 	lg = aaa + aab + aac;
@@ -245,9 +251,9 @@ int HistoGUIad::Draw_Fit(double x_low_win, double y_low_win, double x_hi_win, do
 //		min_y = y[0];
 //hard set graphical boundaries
         max_x = 3.1415;
-		max_y = 2.;
+		max_y = A0*1.5;
 		min_x = -.1;
-		min_y = -.1;
+		min_y = A0*.5;
 /*		for(int i=0; i<x.size(); i++){
 			if(x[i] > max_x) max_x = x[i];
 			if(x[i] < min_x) min_x = x[i];
@@ -338,9 +344,9 @@ int HistoGUIad::DrawData(double x_low_win, double y_low_win, double x_hi_win, do
 //		min_y = y[0];
 //hard set graphical boundaries
         max_x = 3.1415;
-		max_y = 2.;
+		max_y = A0*1.5;
 		min_x = -.1;
-		min_y = -.1;
+		min_y = A0*0.5;
 /*		for(int i=0; i<x.size(); i++){
 			if(x[i] > max_x) max_x = x[i];
 			if(x[i] < min_x) min_x = x[i];
diff --git a/GUI_Base.h b/GUI_Base.h
index 255fb5e..d1a269d 100644
--- a/GUI_Base.h
+++ b/GUI_Base.h
@@ -1,10 +1,12 @@
-#include <X11/Xlib.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <vector>
-#include <cmath> 
+//####################################################################
+//
+// This is a base version of the AD GUI allowing the user to plot two
+// input double vectors. The GUI consists of zooming, crosshair readout, 
+// and drawing on the canvas.  
+//
+//####################################################################
 
+#include "global.h"
 
 class HistoGUI{
 
diff --git a/QDK.h b/QDK.h
index e6b6820..792edb6 100644
--- a/QDK.h
+++ b/QDK.h
@@ -1,3 +1,11 @@
+//#####################################################################
+//
+//This file is a geometric calculation of the efficiency of radiation
+//in germanium crystals as a function of energy, and the crystal
+//geometry of the experiment.
+//
+//#####################################################################
+
 #include "global.h"
 
 using namespace std;
diff --git a/ad.txt b/ad.txt
index 5cdeadd..240cc43 100644
--- a/ad.txt
+++ b/ad.txt
@@ -1,7 +1,7 @@
 Radius = 3 [cm]
 Distance = 4 [cm]
 Thickness = 5 [cm]
-Atten.C = 0.282206 [cm^-1]
-Gamma_E = 1147 [KeV]
-QD2 = 0.802565
-QD4 = 0.44946
+Atten.C = 0.476411 [cm^-1]
+Gamma_E = 426 [KeV]
+QD2 = 0.790549
+QD4 = 0.42078
diff --git a/global.h b/global.h
index 5c10f13..cedeb7d 100644
--- a/global.h
+++ b/global.h
@@ -1,8 +1,10 @@
 #ifndef __iamauniqueid_h__
 #define __iamauniqueid_h__
-
-//define any global data type here.
-
+//########################################################
+//This file is used for defining global data type and all
+//includes needed for the program. 
+//
+//########################################################
 #include <X11/Xlib.h>
 #include <stdio.h>
 #include <cstdio>