diff --git a/acknowledgments.aux b/acknowledgments.aux
index a232ecf347388b7ac8c7462a73f4942775de259a..d2ced5d6a15772bca7c1fbf354afb1809942d153 100644
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+++ b/acknowledgments.aux
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diff --git a/appendix.aux b/appendix.aux
index 35be637e33c13a03637b5c409915fb1c3c3cbf5c..d326ce9a0e9cc71517ce1e5db37842259e9864a1 100644
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diff --git a/appendix.tex b/appendix.tex
index 38af8c46faa60cb8c1c443a7bba795c6658037de..e71889e73ba2d31bc05ff446b640708b9cb4870f 100644
--- a/appendix.tex
+++ b/appendix.tex
@@ -1,6 +1,6 @@
 \chapter*{Appendix}
 \addcontentsline{toc}{chapter}{Appendix}
-\pagenumbering{roman}
+%\pagenumbering{roman}
 %\sectionnumbering{roman} 
 \setcounter{section}{0}
 \renewcommand{\thesection}{\Alph{section}}
@@ -25,6 +25,29 @@ Sensitivity                         & variable*                            \\ \h
 \label{fig:app_lock_in}
 \end{table}
 
+\section{Evaporation parameters} \label{app:evaporation}
+
+\begin{table}[H]
+	\begin{tabular}{|c|c|c|c|c|c|c|}
+		\hline
+		& Time {[}min{]} & FIL {[}A{]} & EMIS {[}mA{]} & FLUX {[}nA{]} & Press. {[}mbar{]} & T {[}°C{]} \\ \hline \hline
+		Evap. 1 & $40$             & $1.75$        & $9.1-6.9$       & $490-540$       &$5.37 \times 10^{-9}$& $24 $                  \\ \hline
+		Evap. 2 & $40$             & $1.75$        & $9.7-5.4$       & $450-530$       &$3.86 \times 10^{-9}$& $24$                   \\ \hline
+		Evap. 3 & $40$             & $1.75$        & $9.5-5.3$       & $470-520$       &$3.21 \times 10^{-9}$& $24$                   \\ \hline
+		Evap. 4 & $40$             & $1.75$        & $10.0-4.9$      & $460-510$       &$2.99 \times 10^{-9}$& $24$                   \\ \hline
+		Evap. 5 & $40$             & $1.75$        & $6.8-4.7$       & $450-500$       &$2.86 \times 10^{-9}$& $24$                   \\ \hline
+	\end{tabular}
+	\caption{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}
+	\label{tab:evaporation_settings}
+\end{table}
+%
+%\begin{figure}[H]
+%    \centering
+%    \includegraphics[width=0.8\linewidth]{img/Evaporation/MaskAlignerChamber_evap.pdf}
+%    \caption{The Mask Aligner chamber configuration during evaporation.}
+%    \label{fig:evaporation_chamber_status}
+%\end{figure}
+
 \section{Walker principle diagram}\label{app:walker_diagram}
 \begin{figure}[H]
     \centering
@@ -38,7 +61,7 @@ Sensitivity                         & variable*                            \\ \h
 
 \includepdf[pages=-,pagecommand={},width=\textwidth,angle=90]{img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf}
 
-\section{New driver electronics}\label{sec:appendix_walker}
+\section{Mask Aligner Walker Commands}\label{sec:appendix_walker}
 The commands need to be sent to the new driver electronics using a serial interface with a baudrate of $115200$ and either new line or carriage return as line end characters. The easiest way to do this is via the Serial Monitor of the Arduino IDE.
 The new driver electronics have the following commands (as of 13.08.24) that can set the driving parameters:
 
@@ -65,6 +88,763 @@ Displays a list of all commands along with short explanations on how to use them
 
 Any of the parameters that can set one of the values can be queried for their current value by using command? (for example pol?). 
 
+\section{Mask Aligner Walker Code}\label{sec:walker_code}
+
+\begin{lstlisting}[basicstyle=\ttfamily\scriptsize, language=C++, xleftmargin=0cm, tabsize=2]
+	
+	#include "DueTimer.h"     // Library used for timing
+	#include "DueFlashStorage.h"  // Probably not needed
+	
+	#define    BAUDRATE         115200  
+	// 115200 baud is reliable
+	#define    FS               (84000000.0/52.0/2.0)   
+	// sampling frequency of dac in dual channel mode
+	#define    PERIODSINGLE     0.00049356      
+	// fitparameters for signal 5500Hz 8th order bessel lowpass
+	#define    TOFFSETSINGLE    0.000085362     
+	// fitparameters for signal 5500Hz 8th order bessel lowpass
+	#define    NSINGLE          382 
+	// approx 0.5ms - 5\% * 0.5 ms of buffer length for dual channel mode
+	#define    NWAVEFORMSINGLE  6   
+	// 2 waveforms = 2 channels + 4 fast channel high/low combinations
+	
+	// Pin for polarity switch 
+	#define    SWITCH_POL       30
+	// pins of the switches for the 4 different channels
+	#define    SWITCH1          22                  //channel Z1       
+	#define    SWITCH2          24                  //channel Z2  
+	#define    SWITCH3          26                  //channel Z3 
+	#define    SWITCH4          28                  //channel X 
+	// pins of the shutters for the 4 different channels
+	#define    SHUTTER1         53                  //channel Z1  
+	#define    SHUTTER2         51                  //channel Z2 
+	#define    SHUTTER3         49                  //channel Z3 
+	#define    SHUTTER4         47                  //channel X 
+	
+	#define    BUFFER_SIZE      256                 // serial buffer character length
+	#define    CR               13
+	#define    LF               10
+	
+	uint32_t  waveform[NWAVEFORMSINGLE][NSINGLE];
+	uint32_t  waveform_zero[NSINGLE];
+	
+	uint32_t  sin_func[NSINGLE];
+	
+	int32_t pulse_buffer = 0;
+	
+	struct Configuration {
+		int8_t output_polarity = 1;   // output_polarity of the signal
+		// for buttons and serial interface  
+		uint8_t amplitude = 100; // amplitude in percent, realized by DAC, 
+		// so affecting output smoothness (int 0 to 100)
+		
+		bool channelZ1 = true; bool channelZ2 = true; 
+		bool channelZ3 = true; bool channelX = true;
+		int32_t max_steps = 10000;
+		uint32_t shutter_idle_time = 5000000;
+	};
+	
+	Configuration configuration;
+	DueFlashStorage dueFlashStorage;
+	
+	char serial_buffer[BUFFER_SIZE];
+	
+	uint8_t save_state_flag = 0;
+	bool no_signal = false;
+	bool shutter_off = false;
+	
+	void turn_on_signal(){
+		no_signal = false;
+		Timer4.detachInterrupt();
+		Timer4.stop();
+		if(configuration.channelZ1)
+		digitalWrite(SHUTTER1, HIGH);
+		if(configuration.channelZ2)
+		digitalWrite(SHUTTER2, HIGH);
+		if(configuration.channelZ3)
+		digitalWrite(SHUTTER3, HIGH);
+		if(configuration.channelX)
+		digitalWrite(SHUTTER4, HIGH);
+		digitalWrite(SWITCH_POL, HIGH);
+		shutter_off = true;
+	}
+	
+	void turn_off_signal(){
+		no_signal = true;
+		next_dac_vector(NSINGLE, waveform_zero);
+		schedule_shutter_on();
+	}
+	
+	void schedule_shutter_on(){
+		Timer4.attachInterrupt(turn_shutter_on).start(configuration.shutter_idle_time);
+	}
+	
+	void turn_shutter_on(){
+		Timer4.detachInterrupt();
+		digitalWrite(SHUTTER1, LOW);
+		digitalWrite(SHUTTER2, LOW);
+		digitalWrite(SHUTTER3, LOW);
+		digitalWrite(SHUTTER4, LOW);
+		shutter_off = false;
+	}
+	
+	void control_switches(){
+		turn_shutter_on();
+		if(configuration.channelZ1)
+		digitalWrite(SWITCH1, HIGH);
+		else
+		digitalWrite(SWITCH1, LOW);
+		
+		if(configuration.channelZ2)
+		digitalWrite(SWITCH2, HIGH);
+		else
+		digitalWrite(SWITCH2, LOW);
+		
+		if(configuration.channelZ3)
+		digitalWrite(SWITCH3, HIGH);
+		else
+		digitalWrite(SWITCH3, LOW);
+		
+		if(configuration.channelX)
+		digitalWrite(SWITCH4, HIGH);
+		else
+		digitalWrite(SWITCH4, LOW);
+		
+	}
+	
+	void delayed_switch_pol_high(){
+		digitalWrite(SWITCH_POL, HIGH);
+		Timer2.stop();
+	}
+	
+	void delayed_switch_pol_low(){
+		digitalWrite(SWITCH_POL, LOW);
+		Timer2.stop();
+	}
+	
+	//Inelegant but functional and probably still very fast
+	int8_t polarity_table(uint8_t x, uint8_t y){        
+		if(x == 0 && y == -1)
+		return 0;
+		else if(x == 0 && y == 1)
+		return 1;
+		else if(x == 1 && y == -1)
+		return 1;
+		else if(x == 1 && y == 1)
+		return 0;
+	}
+	
+	uint8_t state = 0;
+	const uint8_t FIRST = 0; const uint8_t NORMALDOWN = 1; const uint8_t  NORMALUP = 2; 
+	const uint8_t  LAST = 3; const uint8_t  STOP = 4;
+	
+	int8_t last_sig;
+	const uint8_t polarity_delay = 25;
+	
+	//State machine driving the pulses 
+	//Pulse is made up of 6 possible parts:
+	//Curve from -3.3 to 3.3 V
+	//Curve from 3.3 to -3.3 V
+	//Curve from 0 to 3.3 V and vice versa for start and end pulses
+	//Curve from 0 to -3.3 V and vice versa
+	void pulse_start(){
+		switch (state)
+		{
+			case FIRST: //First pulse
+			if(abs(pulse_buffer) > 0){
+				turn_on_signal();
+				if(shutter_off){
+					Timer3.stop();
+					delayMicroseconds(16383);
+					Timer3.start(500);
+				}
+				digitalWrite(SWITCH_POL, LOW);
+				next_dac_vector(NSINGLE, waveform[2 + 
+					polarity_table(configuration.output_polarity, signum(pulse_buffer))]);
+				last_sig = signum(pulse_buffer);
+				pulse_buffer -= signum(pulse_buffer);
+				state = pulse_buffer == 0 ? LAST : NORMALDOWN;
+			}
+			break;
+			
+			case NORMALDOWN: //Switch pulse ON
+			next_dac_vector(NSINGLE, waveform[1 - 
+				polarity_table(configuration.output_polarity, signum(pulse_buffer))]);
+			if(polarity_delay == 0)
+			digitalWrite(SWITCH_POL, HIGH);
+			else
+			Timer2.attachInterrupt(delayed_switch_pol_high).start(polarity_delay);
+			state = NORMALUP;
+			break;
+			
+			case NORMALUP: //Switch pulse OFF
+			next_dac_vector(NSINGLE, waveform[0 + 
+				polarity_table(configuration.output_polarity, signum(pulse_buffer))]);
+			last_sig = signum(pulse_buffer);
+			if(pulse_buffer != 0)
+			pulse_buffer -= signum(pulse_buffer);
+			if(polarity_delay == 0)
+			digitalWrite(SWITCH_POL, LOW);
+			else
+			Timer2.attachInterrupt(delayed_switch_pol_low).start(polarity_delay);
+			state = pulse_buffer == 0 ? LAST : NORMALDOWN;
+			break;
+			
+			case LAST: //Last pulse
+			next_dac_vector(NSINGLE, waveform[5 - 
+				polarity_table(configuration.output_polarity, last_sig)]);
+			if(polarity_delay == 0)
+			digitalWrite(SWITCH_POL, HIGH);
+			else
+			Timer2.attachInterrupt(delayed_switch_pol_high).start(polarity_delay);
+			state = STOP;
+			break;
+			
+			case STOP: //Switch pulse ON
+			//Timer2.attachInterrupt(delayed_switch_pol_low).start(polarity_delay);
+			state = FIRST;
+			turn_off_signal();
+			break;
+		}
+		
+	}
+	
+	void setup() {
+		//put your setup code here, to run once:
+		Serial.begin(BAUDRATE);
+		Serial.setTimeout(50);
+		switch_setup();
+		dac_timer_setup();
+		dac_setup();
+		turn_shutter_on();
+		
+		//Run timer that times pulses for 1kHz
+		Timer3.attachInterrupt(pulse_start).start(500);
+		//generate_sin();
+		generate_waveforms();
+		control_switches();
+	}
+	
+	void switch_setup (){
+		pinMode(SWITCH1, OUTPUT);
+		pinMode(SWITCH2, OUTPUT);
+		pinMode(SWITCH3, OUTPUT);
+		pinMode(SWITCH4, OUTPUT);
+		pinMode(SWITCH_POL, OUTPUT);
+		
+		pinMode(SHUTTER1, OUTPUT);
+		pinMode(SHUTTER2, OUTPUT);
+		pinMode(SHUTTER3, OUTPUT);
+		pinMode(SHUTTER4, OUTPUT);
+		
+		digitalWrite(SWITCH1, LOW);
+		digitalWrite(SWITCH2, LOW);
+		digitalWrite(SWITCH3, LOW);
+		digitalWrite(SWITCH4, LOW);
+		
+		digitalWrite(SHUTTER1, LOW);
+		digitalWrite(SHUTTER2, LOW);
+		digitalWrite(SHUTTER3, LOW);
+		digitalWrite(SHUTTER4, LOW);
+	}  
+	//////////////////////////////////////////////////////////
+	//
+	//    DAC RELATED FUNCTIONS
+	//
+	//////////////////////////////////////////////////////////
+	
+	void dac_timer_setup (){
+		//The following creates a 84/52MHz square wave on 
+		//PWM pin 2 with 50% dutycycle. It drives the DAC conversions
+		pmc_enable_periph_clk(TC_INTERFACE_ID + 0 * 3 + 0); // clock the TC0 channel 0
+		
+		TcChannel * t = &(TC0->TC_CHANNEL)[0];   
+		// pointer to TC0 registers for its channel 0
+		t->TC_CCR = TC_CCR_CLKDIS;               
+		// disable internal clocking while setup regs
+		t->TC_IDR = 0xFFFFFFFF;                  
+		// disable interrupts
+		t->TC_SR;                                
+		// read int status reg to clear pending
+		t->TC_CMR = TC_CMR_TCCLKS_TIMER_CLOCK1 | 
+		// use TCLK1 (prescale by 2, = 42MHz)
+		TC_CMR_WAVE |                
+		// waveform mode
+		TC_CMR_WAVSEL_UP_RC |        
+		// count-up PWM using RC as threshold
+		TC_CMR_EEVT_XC0 |            
+		// Set external events from XC0 (this setup TIOB as output)
+		TC_CMR_ACPA_CLEAR | TC_CMR_ACPC_CLEAR |
+		TC_CMR_BCPB_CLEAR | TC_CMR_BCPC_CLEAR;
+		
+		t->TC_RC = 26; // counter resets on RC, so sets period in terms of 42MHz clock
+		t->TC_RA = 13; // square wave
+		t->TC_CMR = (t->TC_CMR & 0xFFF0FFFF) | TC_CMR_ACPA_CLEAR | TC_CMR_ACPC_SET;  
+		// set clear and set from RA and RC compares
+		t->TC_CCR = TC_CCR_CLKEN | TC_CCR_SWTRG;   
+		// re-enable local clocking and switch to hardware trigger source.
+	}
+	
+	void dac_setup (){
+		pmc_enable_periph_clk (DACC_INTERFACE_ID) ; // start clocking DAC
+		dacc_reset(DACC);
+		dacc_set_transfer_mode(DACC, 1); 
+		// write to both channels in word mode
+		dacc_set_power_save(DACC, 0, 1);            // sleep = 0, fastwkup = 1
+		dacc_set_analog_control(DACC, DACC_ACR_IBCTLCH0(0x02) 
+			| DACC_ACR_IBCTLCH1(0x02) | DACC_ACR_IBCTLDACCORE(0x01)); 
+		//For DAC frequency > 500 KHz !?!?!?!?!
+		dacc_set_trigger(DACC, 1); 
+		//TIO Output of the Timer Counter Channel 0
+		dacc_set_timing(DACC, 1, 0, 8); 
+		//uint32_t  ul_refresh (refresh minimum seems to be 1024*1/42=24mus
+		//, uint32_t  ul_maxs, uint32_t  ul_startup (startup is set to 512 dac clocks = 12mus)
+		
+		dacc_enable_channel(DACC, 0);
+		dacc_enable_channel(DACC, 1);
+		dacc_enable_flexible_selection(DACC);
+		
+		NVIC_DisableIRQ(DACC_IRQn);
+		NVIC_ClearPendingIRQ(DACC_IRQn);
+		NVIC_EnableIRQ(DACC_IRQn);
+		
+		DACC->DACC_PTCR =  DACC_PTCR_TXTEN;  
+		// Enable PDC Transmit channel request
+		
+		uint32_t zero_dual_dac = (0 << 12) | 0 | (0 << 16) | (1 << 28); 
+		// bit 12 selects dac0, bits 0-11 give value,
+		// bit 28 selects dac1, bits 16-27 give value
+		next_dac_vector(1, &zero_dual_dac); 
+	}
+	
+	void next_dac_vector(int nwave, uint32_t *wave){
+		DACC->DACC_TNPR = (uint32_t)  wave; // DMA buffer
+		DACC->DACC_TNCR = nwave;
+	}
+	
+	void generate_sin(){
+		
+		for (int i=0; i < NSINGLE; i++){
+			double t = i/FS+TOFFSETSINGLE;
+			const double off = 100/FS;
+			
+		}
+	}
+	
+	void generate_waveforms(){
+		
+		// we generate waveform data for dual dac channels
+		const uint32_t chsel = (0<<12) | (1<<28); //mask for lower bits dac0, higher bits dac1
+		
+		double ch1 = 0;
+		double ch2 = 0;
+		
+		double ch1_fast = 0;
+		double ch2_fast = 0;
+		
+		for (int i=0; i < NSINGLE; i++){
+			double t = i/FS+TOFFSETSINGLE;
+			const double off = 100/FS;
+			
+			//rising slope. Equation calculated by Marcus Liebmann. 
+			//Acceleration is continuous sine.
+			if(t <= off) ch1 = 0.00;
+			else if ((t - off) <= PERIODSINGLE) ch1 = 0.01 * configuration.amplitude * 
+			4095.0 * (-1.0/(2.0*PI) * sin(2.0 * PI * 
+				(t - off)/PERIODSINGLE) + (t - off)/PERIODSINGLE);
+			else ch1 = 0.01 * configuration.amplitude * 4095.0;
+			ch2 = 0.01 * configuration.amplitude * 4095.0 - ch1;
+			//Flat Wave fore zeroing
+			waveform_zero[i] =  0 | 0 << 16 | chsel;
+		}
+		
+	}
+	
+	//////////////////////////////////////////////////////////
+	//
+	//    SERIAL COMMANDS (VISA STYLE)
+	//
+	//////////////////////////////////////////////////////////
+	
+	
+	void process_serial_byte(char c){
+		if (c == CR || c == LF) {
+			
+			if (strlen(serial_buffer) > 0) {
+				parse_command(serial_buffer);
+			}
+			
+			reset_buffer();
+			
+		}
+		else if (c > 32 && c < 127) {
+			add_to_buffer(c);
+		}
+	}
+	
+	void reset_buffer() {
+		memset(&serial_buffer[0], 0, sizeof(serial_buffer));
+	}
+	
+	void add_to_buffer(char c) {
+		
+		if (strlen(serial_buffer) >= BUFFER_SIZE - 1) {
+			
+			reset_buffer();
+			append_char(serial_buffer, c);
+			
+		}
+		else {
+			
+			append_char(serial_buffer, c);
+			
+		}
+	}
+	
+	void append_char(char* s, const char c) {
+		
+		const int len = strlen(s);
+		
+		if (len < BUFFER_SIZE - 1) {
+			s[len] = c;
+			s[len + 1] = '\0';
+		}
+	}
+	
+	void parse_command(char *command) {
+		// Split command at semicolons
+		char *ptr;
+		ptr = strtok(command, ";");
+		
+		// The value is going to be used for sscanf
+		int32_t value;
+		
+		// Parse commands
+		while (ptr != NULL) {
+			// Identification
+			if (strcasecmp(ptr, "*idn?") == 0)                            
+				Serial.println("MAW 0113"); 
+				//This is the old identification change when ID is known
+			
+			// Query
+			else if (strcasecmp(ptr, "pulse?") == 0)                      
+				Serial.println(abs(pulse_buffer) > 0);
+			else if (strcasecmp(ptr, "pol?") == 0)                        
+				Serial.println(configuration.output_polarity);
+			else if (strcasecmp(ptr, "amp?") == 0)                        
+				Serial.println(configuration.amplitude);
+			else if (strcasecmp(ptr, "volt?") == 0)                       
+				Serial.println((double) configuration.amplitude * 1.2);
+			else if (strcasecmp(ptr, "ch?") == 0)                         
+			{Serial.print("[ "); Serial.print(configuration.channelZ1); 
+				Serial.print(" "); Serial.print(configuration.channelZ2); 
+				Serial.print(" "); Serial.print(configuration.channelZ3); 
+				Serial.print(" "); Serial.print(configuration.channelX); 
+				Serial.println(" ]");}
+			else if (strcasecmp(ptr, "channel?") == 0)                   
+			 {Serial.print("[ "); Serial.print(configuration.channelZ1); 
+			 	Serial.print(" "); Serial.print(configuration.channelZ2); 
+			 	Serial.print(" "); Serial.print(configuration.channelZ3); 
+			 	Serial.print(" "); Serial.print(configuration.channelX); 
+			 	Serial.println(" ]");}
+			else if (strcasecmp(ptr, "maxsteps?") == 0)                   
+				Serial.println(configuration.max_steps);
+			else if (strcasecmp(ptr, "maxmstep?") == 0)                   
+				Serial.println(configuration.max_steps);
+			
+			// Set
+			else if (sscanf (ptr,"pol%i%99[^\n]",&value) == 1)            
+				configuration.output_polarity = validate_polarity(value);
+			else if (sscanf (ptr,"amp%i%99[^\n]",&value) == 1)            
+				configuration.amplitude = validate_amplitude(value);
+			else if (sscanf (ptr,"volt%i%99[^\n]",&value) == 1)          
+				configuration.amplitude = validate_voltage(value);
+			else if (sscanf (ptr,"step%i%99[^\n]",&value) == 1)          
+				pulse_buffer = validate_single_step(value);
+			else if (sscanf (ptr,"mstep%i%99[^\n]",&value) == 1)          
+				pulse_buffer = validate_multi_step(value);
+			else if (sscanf (ptr,"steps%i%99[^\n]",&value) == 1)          
+				pulse_buffer = validate_multi_step(value);
+			else if (sscanf (ptr,"channel%x%99[^\n]", &value) == 1)       
+				set_channel(value); else if (sscanf (ptr,"ch%x%99[^\n]", &value) == 1)  
+					set_channel(value);
+			
+			//Abort signal
+			else if (strcasecmp(ptr, "cancel") == 0)                      
+				{stop_current_pulse_sequence();} else if (strcasecmp(ptr, "stop") == 0)                
+				{stop_current_pulse_sequence();}  else if (strcasecmp(ptr, "abort") == 0)               
+				{stop_current_pulse_sequence();}
+			else if (sscanf (ptr,"maxmstep%i%99[^\n]",&value) == 1)       
+				configuration.max_steps = validate_multi_step_max(value);
+			else if (sscanf (ptr,"maxmsteps%i%99[^\n]",&value) == 1)      
+				configuration.max_steps = validate_multi_step_max(value);
+			
+			// Help
+			else if (strcasecmp(ptr, "help") == 0)                {print_help();}
+			
+			// Save the state
+			if (save_state_flag){      
+				save_state_flag = 0;
+				save_state();
+			}
+			
+			// Move command pointer
+			ptr = strtok(NULL, ";");
+		}
+	}
+	
+	
+	//////////////////////////////////////////////////////////
+	//
+	//    Validate Parsed inputs
+	//
+	//////////////////////////////////////////////////////////
+	
+	void stop_current_pulse_sequence(){
+		Serial.println("Aborting pulse sequence!");
+		pulse_buffer = 0;
+		turn_off_signal();
+	}
+	
+	void print_help(){
+		Serial.println("\"pulse?\" queries if there is currently a
+			 pulse running. Returns 0 (false) or 1 (true)");
+		Serial.println("\"pol?\" queries current polarization direction.");
+		Serial.println("\"amp?\" queries current pulse amplitude.");
+		Serial.println("\"volt?\" queries current pulse voltage.");
+		Serial.println("\"channel?\" queries current channels status 
+			order Z1 Z2 Z3 X. 0 is off 1 is on.");
+		Serial.println("\"maxmstep?\" queries current maximum allowed
+			steps for the mstep function. Aliases: \"maxsteps?");
+		
+		Serial.println("\"polx\" changes the current polarization direction.
+			 Accepted values: 1,-1");
+		Serial.println("\"amp x\" changes the current amplitude of 
+			the signal (100 = 120 V). 
+		Accepted values: 0 to 100");
+		Serial.println("\"volt x\" changes the current amplitude as a 
+			voltage value. 
+		This gives only approximate Voltages due to integer conversion.
+			Maximal conversion error is +- 0.5 V Accepted values: 0 to 120.");
+		Serial.println("\"step x\" drives single step. Accepted values: 1,-1");
+		Serial.println("\"mstep x\" drives multiple steps consecutively. 
+			Aliases: \"steps x\", Default accepted values: -10000 to 10000");
+		Serial.println("\"maxmstep x\" changes the maximum allowed 
+			steps for the mstepfunction. 
+		Aliases: \"maxsteps. Default: 10000");
+		Serial.println("\"channel x\" changes channels to state x. 
+			x is a bitmask Z1|Z2|Z3|X. 
+		0 is off 1 is on. So turning on channels 1 and 3 would be 
+			1010. Aliases: \"ch x\"
+		Accepted values: x:0000 to 1111 in binary");
+		
+		Serial.println("\"cancel\" stops all current pulses. 
+			Will finish the currently running pulse.
+		Aliases: \"stop\", \"abort\"");
+		Serial.println("\"help\" shows this information.");
+	}
+	//Value is read as a hexadecimal input value in the form 0000 
+	//then it checks every forth digit which responds to doing binary 
+	//comparison digit by digit for value and assigns motors
+	void set_channel(int value){
+		if (pulse_buffer != 0) {
+			Serial.println("Error: Wait for current steps to finish!");
+			return;
+		}
+		if(value > 4369 || value < 0){
+			Serial.println("Error: Invalid value for x in \"channel\" command!");
+			return;
+		}
+		configuration.channelX = (value & (1 << 0)) == 1;
+		configuration.channelZ3 = (value & (1 << 4)) == 16;
+		configuration.channelZ2 = (value & (1 << 8)) == 256;
+		configuration.channelZ1 = (value & (1 << 12)) == 4096;
+		
+		control_switches();
+		
+			Serial.print("Setting channel to: ");
+			Serial.print("[ "); Serial.print(configuration.channelZ1); 
+			Serial.print(" "); Serial.print(configuration.channelZ2); 
+			Serial.print(" "); Serial.print(configuration.channelZ3); 
+			Serial.print(" "); 
+			Serial.print(configuration.channelX); Serial.println(" ]");
+			Serial.print("[ "); Serial.print(configuration.channelZ1); 
+			Serial.print(" "); Serial.print(configuration.channelZ2); 
+			Serial.print(" "); Serial.print(configuration.channelZ3); 
+			Serial.print(" "); Serial.print(configuration.channelX); 
+			Serial.println(" ]");
+	}
+	
+	uint8_t validate_polarity(int value){
+		
+		if (abs(value) != 1) {
+			Serial.println("Error: Invalid polarity!");
+			return configuration.output_polarity;
+		}
+		save_state_flag = 1;
+		Serial.print("Polarity changed to: ");
+		Serial.println(value == 1);
+		return (uint8_t) value == 1;
+	}
+	
+	uint8_t validate_amplitude(int value){
+		
+		if (value < 0 || value > 100) {
+			Serial.println("Error: Invalid amplitude!");
+			return configuration.amplitude;
+		}
+		
+		configuration.amplitude = (uint8_t) value;
+		generate_waveforms();
+		save_state_flag = 1;
+		Serial.print("Amplitude changed to: ");
+		Serial.println(value);
+		return (uint8_t) value;
+	}
+	
+	uint8_t validate_voltage(int value){
+		
+		if (value < 0 || value > 120) {
+			Serial.println("Error: Invalid voltage!");
+			return configuration.amplitude;
+		}
+		
+		uint8_t amp = round((double) value * 0.83333);
+		if(amp > 120)
+		amp = 120;
+		
+		configuration.amplitude = amp;
+		generate_waveforms();
+		save_state_flag = 1;
+		Serial.print("Amplitude changed to: ");
+		Serial.println(amp);
+		Serial.print("Voltage changed to: ");
+		Serial.println((double) amp * 1.2);
+		return (uint8_t) amp;
+	}
+	
+	int32_t validate_multi_step(int value){
+		
+		if (pulse_buffer != 0) {
+			Serial.println("Error: Wait for current steps to finish!");
+			return pulse_buffer;
+		}
+		if (abs(value) > configuration.max_steps) {
+			Serial.println("Error: Invalid value for
+				 \"mstep\" command! Larger than allowed maximum!");
+			return pulse_buffer;}
+		Serial.print("Stepping: ");
+		Serial.print(value);
+		Serial.println(" steps");
+		return (int32_t) value;  
+	}
+	
+	int32_t validate_multi_step_max(int32_t value){
+		
+		if (value < 0) {
+			Serial.println("Error: Invalid value for 
+				\"maxmstep\" command!");
+			return pulse_buffer;}
+		Serial.print("Setting new max_step: ");
+		Serial.print(value);
+		Serial.println(" steps");
+		return (int32_t) value;  
+	}
+	
+	int16_t validate_single_step(int value){
+		
+		if (pulse_buffer != 0) {
+			Serial.print("Error: Wait for current steps to finish!");
+			return pulse_buffer;
+		}
+		if (value != -1 && value != 1) {
+			Serial.print("Error: Invalid value for 
+				\"step\" command!");
+			return pulse_buffer;}
+		//return (int16_t) (value * configuration.pulses_per_trigger);
+		Serial.print("Stepping: ");
+		Serial.println("single step");
+		return (int16_t) (value); 
+	}
+	
+	int32_t validate_idle_time(int value){
+		
+		if (value < 0) {
+			Serial.println("Error: Invalid value for 
+				\"idletime\" command! Only positive numbers!");
+			return pulse_buffer;
+		}
+		if (value < 100000) {
+			Serial.println("Error: Invalid value for 
+				\"idletime\" command! Value chosen too small!");
+			return pulse_buffer;
+		}
+		Serial.print("Setting idle timer to: ");
+		Serial.println(value);
+		return (int32_t) value;  
+	}
+	
+	//////////////////////////////////////////////////////////
+	//
+	//    SAVE AND RECALL STATE
+	//
+	//////////////////////////////////////////////////////////
+	
+	//unused
+	void save_state(){
+		
+		byte config_bytes[sizeof(Configuration)]; 
+		// create byte array to store the struct
+		memcpy(config_bytes, &configuration, sizeof(Configuration)); 
+		// copy the struct to the byte array
+		dueFlashStorage.write(4, config_bytes, sizeof(Configuration)); 
+		// write byte array to flash at address 4
+	}
+	//unused
+	void recall_state(){
+		
+		if (dueFlashStorage.read(0)){ //codeRunningForTheFirstTime 
+			dueFlashStorage.write(0, 0);
+			save_state();
+			return;
+		}
+		
+		byte* config_bytes = dueFlashStorage.readAddress(4); 
+		// byte array which is read from flash at adress 4
+		Configuration cff; // create a temporary struct
+		memcpy(&cff, config_bytes, sizeof(Configuration)); 
+		// copy byte array to temporary struct
+		
+		// validate
+		if (cff.output_polarity == 1 || cff.output_polarity == -1) 
+			configuration.output_polarity = cff.output_polarity;
+		if (cff.amplitude >= 0 && cff.amplitude <= 100) 
+			configuration.amplitude = cff.amplitude;
+	}
+	
+	void loop() {
+		// Read serial port commands
+		if (Serial.available())  {
+			process_serial_byte(Serial.read());
+		}
+		
+		// Read serial port commands
+		//pulse_buffer = Serial.parseInt();
+	}
+	
+	//////////////////////////////////////////////////////////
+	//
+	//    Auxillary and helper functions
+	//
+	//////////////////////////////////////////////////////////
+	
+	int signum(int x) { 
+		return (x > 0) - (x < 0);
+	}
+	
+\end{lstlisting}
+
+
 \section{Raycast Simulation}\label{sec:appendix_raycast}
 The ray casting simulation takes the following parameters:
 
diff --git a/bibliography.aux b/bibliography.aux
index e756489aa09c939ba9b292c9b5fc860b919f0c33..f2c0101d8f51bc4f2255fb6a12633f8177321b9a 100644
--- a/bibliography.aux
+++ b/bibliography.aux
@@ -14,7 +14,7 @@
 \bibcite{tungsten_evaporation}{{10}{}{{}}{{}}}
 \bibcite{afm_physics}{{11}{}{{}}{{}}}
 \bibcite{afm_bio}{{12}{}{{}}{{}}}
-\@writefile{toc}{\contentsline {chapter}{Bibliography}{74}{chapter*.82}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Bibliography}{73}{chapter*.77}\protected@file@percent }
 \bibcite{SEM_image_01}{{13}{}{{}}{{}}}
 \bibcite{SEM_image_02}{{14}{}{{}}{{}}}
 \bibcite{SEM_book}{{15}{}{{}}{{}}}
@@ -26,9 +26,10 @@
 \bibcite{arduino_cpu_datasheet}{{21}{}{{}}{{}}}
 \bibcite{switch_datasheet}{{22}{}{{}}{{}}}
 \bibcite{torr_seal}{{23}{}{{}}{{}}}
-\bibcite{grain_growth}{{24}{}{{}}{{}}}
+\bibcite{Simon}{{24}{}{{}}{{}}}
+\bibcite{grain_growth}{{25}{}{{}}{{}}}
 \@setckpt{bibliography}{
-\setcounter{page}{77}
+\setcounter{page}{76}
 \setcounter{equation}{1}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -37,27 +38,27 @@
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diff --git a/bibliography.bib b/bibliography.bib
index 2ff11fece7abb4be21fc3fa2500ae4d7f6a68682..8fdcbfdbb6f73acf7d97c4386228770b8ba0f802 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -339,4 +339,19 @@ lastchecked = {2024-10-01}
 	howpublished = {\url{https://www.agilent.com/cs/library/datasheets/public/data-sheet-torr-seal-products-5994-5102-en-agilent.pdf}},
 	year = {2022},
 	note = {[Accessed 02-10-2024]},
-}
\ No newline at end of file
+}
+
+@thesis{Simon,
+	author = {Mathioudakis, Simon},
+	title = {{I}nbetriebnahme und {T}est eines {M}ask
+	{A}ligners für {U}ltrahochvakuum},
+	school       = {RWTH Aachen University},
+	type         = {Bachelors},
+	address      = {Aachen},
+	publisher    = {RWTH Aachen University},
+	year         = {2015},
+	note         = {unpublished, but viewable on the Server of the 2nd institute of physics B},
+}
+
+Inbetriebnahme und Test eines Mask
+Aligners für Ultrahochvakuum
\ No newline at end of file
diff --git a/chap01.aux b/chap01.aux
index 291f03014d6ce5084309aeea4b27014730aa7b8e..90d66f5b0ab1fe787164b783e5b7f8d8024db71b 100644
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+\newlabel{fig:sem_setup}{{1.22}{31}{The beam path for an SEM (\subref {fig:sem_setup_beam}). The three detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite {SEM_image_01} and ~\cite {SEM_image_02}}{figure.caption.32}{}}
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diff --git a/chap01.tex b/chap01.tex
index f46455ab03439859610d25af87b23e4d6a4fcc75..47ca0d3d9e29abbb03623d512b47d07dc5b6e3cc 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -1,48 +1,14 @@
 % !TeX spellcheck = <en-US>
 \chapter{Mask Aligner background} \label{ch:background}
-The Mask Aligner is used to create thin patterned films on samples with high accuracy. This chapter will introduce the required background behind the evaporation and explain the basic evaporation and alignment setup.
+The Mask Aligner is used to create thin patterned films on samples with high accuracy. This chapter summarizes the prerequisite knowledge for the fabrication and analysis techniques used in this thesis. 
 
-\section{Electron beam evaporation}
-\todo{Cut chapter?}
-Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique that in \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) deposits material onto a substrates surface.
-
-\begin{figure}[H]
-    \centering
-    \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
-    \caption{Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }
-    \label{fig:e-beam_evap}
-\end{figure}
- 
-The setup of an electron beam evaporator is shown in Figure \ref{fig:e-beam_evap}. The source material is placed inside a tungsten crucible as pellets of ultrapure ($>99$ \%) material.
-%The crucible is also heated during the evaporation process, in order to prevent it from being damaged, a material with a high melting point is chosen. Tungsten with a melting point of 3695 K ~\cite{Tungsten_melt} is usually chosen. 
-%Additionally, the crucible usually has to be water cooled to avoid outgassing during the evaporation process.
-
-In order to heat the source material it is hit with a high voltage electron beam ($\mathcal{O}$($1$~kV)), emitted by either an electron gun or a filament. This beam usually is focused using magnetic fields to hit the source material. Energy transfer heats the hit atoms and eventually leads to the evaporation according to its vapor pressure.\\
-
-%The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)~\cite{CASINO} so the heating occurs only very near to the source material's surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
-
-When the material's vapor pressure exceeds the surrounding environments pressure, a vapor forms. The sample is kept at a temperature much colder than the source material's temperature, due to this the material beam will condense on the substrate's surface forming a thin film. \\
-
-In order to ensure the material beam reaches the sample in a direct path, the mean free path (MFP) of a traveling particle has to be larger than the distance to the sample's surface. For this reason, high vacuum (HV) (MFP of $10$ cm to $1$ km) or ultra-high vacuum conditions (UHV) (MFP of $1$ km to $10^5$ km) are used.
-
-The deposition rate of the evaporator can be measured using a molecular flux monitor. The deposition rate of a material is described by the Hertz-Knudsen equation:
-\begin{equation}
-	\frac{dN}{A dt} = \frac{\alpha (p_\text{e} - p)}{\sqrt{2 \pi m k_\text{B} T}}
-	\label{eq:hertz_knudsen}
-\end{equation}
-
-where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$ is time, $\alpha$ is the sticking coefficient, $p$ is the gas pressure of the impinging gas, $m$ is the mass of a single particle, $k_\text{B}$ is the Boltzmann constant, $p_\text{e}$ is the vapor pressure of the material at the sample temperature and $T$ is the temperature~\cite{knudsen}. The sticking parameter of a material can be looked up in literature. With this, the total deposition rate can then be estimated. In practice since the pressure of the impinging gas is difficult to determine this is difficult to estimate, since it requires precise knowledge on the temperature of the source, that is typically not measured. Instead, usually calibration evaporations are performed for different heating powers and different times to determine the deposition rate for a given setup.
-
-Comparing e-beam evaporation with so-called sputtering of material onto a surface, it offers more controlled deposition~\cite{Vapor_depo_princ}. In sputtering, high energy particles are produced hitting the sample, which can lead to local roughening~\cite{sputter_damage}.
-In contrast to thermal evaporation, where the source is typically heated by Joule heating from a resistive current, higher temperatures are available with e-beam evaporation. This is required, e.g. for \ce{NB}~\cite{tungsten_evaporation}.
-A shutter is used to control the controls the deposition of the material.
 
 \section{Stencil lithography}
-Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is typically made of a membrane of \ce{SiN} that is patterned with a lithography process, such as electron beam lithography. Using e-beam lithography, masks can be produced at sub micrometer scales. \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material. The mask is placed closed to the substrates surface. The molecular beam only reaches the sample through holes in the mask. In this way, a pattern is transferred from the mask to the sample. \\
+Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is typically made of a membrane that is patterned with a lithography process, such as electron beam lithography. Using e-beam lithography, masks can be produced at sub micrometer scales. \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material. The mask is placed closed to the substrates surface. The molecular beam of evaporated materials only reaches the sample through holes in the mask. In this way, a pattern is transferred from the mask to the sample. \\
 Stencil Lithography can also be used for etching where patterns are carved into the substrate's surface, using reactive ion etching. \\
 Stencil lithography requires no resist or other chemical treatment of the sample and thus protects it from possible contamination. Masks can also be reused many times. The process is relatively simple and fast. In stencil lithography, the fabrication speed is only limited by the possible deposition rate and the complexity of applying the mask to the sample. \\
-While versatile since many patterns can be deposited or etched, stencil lithography comes with challenges. 
-Material is also deposited on the masks including in the aperture of the mask, which reduces its effective size over time. This means that while masks can be reused, they cannot be reused indefinitely.
+While versatile, since many patterns can be deposited or etched, stencil lithography comes with challenges. 
+Material is also deposited on the masks including the side walls of the apertures of the mask, which reduces its effective size over time, an effect referred to as clogging. This means that while masks can be reused, they cannot be reused indefinitely.
 One of the biggest challenges is that in order to get sharp patterns on the substrates surface, the mask has to be placed directly on the surface of the sample. Otherwise effects resulting from the aperture of the molecular beam result in a "blurring" of the intended structures. However, direct placement of the mask on the substrates surface can contaminate or damage both mask and sample. It should be avoided when measurements in devices highly sensitive to contaminants such as \textbf{S}canning \textbf{T}unneling \textbf{M}icroscopes (STMs) is intended. \\
 
 The Mask Aligner in this work is a tool designed to overcome the challenge of sample mask alignment. It allows precise control of mask sample distance and angle. 
@@ -68,11 +34,10 @@ The width of the penumbra $p$ is determined by the distance of the crucible to t
 When using stencil lithography, the penumbra should be as small as possible. The target penumbra for the mask aligner used in this thesis is $< 100$ nm~\cite{Bhaskar}. A certain size is required for the crucible to be able to evaporate lead efficiently. The distance to the beam source cannot be increased indefinitely since the amount of material deposited on the sample falls off with the square of $d$. For our setup, these quantities are: $b\approx6$ mm, $l\approx25$ cm. For a desired $p < 100$ nm a distance between mask and sample of at most $d\approx4$ $\mu$m is needed.\\
 
 \subsubsection{Tilt induced penumbra}
-Formerly, the model for the penumbra assumed perfect alignment between mask and sample, but potentially large distance $d$. Additionally the distance on one side of the mask can be larger than that on the other. 
+Formerly, the model for the penumbra assumed perfect alignment between mask and sample. However, if the mask is tilted with respect to the sample, the distance on one side of the mask can be larger than that on the other. 
 
-This results in $2$ different penumbral lengths $p_1$ and $p_2$ along the major axis of the tilt, an illustration of this can be seen in Figure \ref{fig:penumbra_explanation_tilt_2d}. Along other 
-
-any other axis of the tilt, however, this will result in two new distances $d_1 '> d_1$ and $d_2 '< d_2$. This can be continued along a half circle until $d_1 ' = d_2 '$ where we have the situation similar to the aligned case again. This results in a penumbra, as shown in Figure \ref{fig:penumbra_explanation_tilt_sim}.\\
+This results in $2$ different penumbral lengths $p_1$ and $p_2$ along the major axis of the tilt, an illustration of this can be seen in Figure \ref{fig:penumbra_explanation_tilt_2d}.
+This results in an elliptical penumbra, as shown in Figure \ref{fig:penumbra_explanation_tilt_sim}.\\
 
 \begin{figure}[H]
     \centering
@@ -92,6 +57,8 @@ any other axis of the tilt, however, this will result in two new distances $d_1
 
 Since the evaporation effectively gives a projection of a circle through an aperture, the resulting image is a conical section. If alignment is imperfect the projection will be an ellipse.
 
+\input{chap02}
+
 \section{Measurement techniques}
 In the following, the techniques used in this thesis and their working principles will be explained.
 \subsection{Atomic Force Microscopy}
@@ -123,18 +90,22 @@ The most intuitive mode is contact mode.
 In contact mode the sample is directly contacted by the cantilever. This is achieved by applying a constant force to the surface with the cantilever. When passing over a higher feature of the samples surface the cantilever will bend and this deflection is measured with the laser diode. When this occurs, the z piezo is adjusted until the previous bending is restored. This restoration of bending is the feedback loop of contact mode (see Fig. \ref{fig:afm_principle}). By measuring the needed z adjustment, a height map of the sample is recorded. \\
 The main disadvantage of contact mode is that the constant force can damage the surface and the cantilever. One can even use contact mode to scratch the sample's surface in specific locations to write patterns into the surface. \\
 In this thesis, however, both damage to cantilever and sample was minimized, which is why contact mode is not used.
+
 \paragraph{Non-Contact}
 Another mode is non-contact mode. In this mode, the cantilever does not touch the sample at all. Instead, the attractive potential of the sample surface to the cantilever is used to map the topography. In order to accomplish this the cantilever is oscillated near the samples surface close to its natural resonance frequency. When the cantilever approaches the samples surface its resonance frequency is shifted to lower value, in each oscillation cycle. This causes the oscillation amplitude to decrease with distance to the samples surface. When the tip sample distance increases the opposite happens. \\
 Either one can use phase or amplitude to determine deviations from the resonance frequency of the cantilever. By either keeping the phase between driving and response at 90° or the amplitude of the cantilever oscillation at constant excitation. Both are accomplished by moving the z piezo as the cantilever is moved across the sample. This is the feedback loop for non-contact mode. The feedback from the laser diode measurement drives the signal given to the z piezo to constantly keep the same tip sample distance.\\
 While non-contact mode damages the tip and the sample less. It comes with the cost of added difficulty since the potential in the non-contact regime is relatively flat. Due to this feedback loop signal is small. Additionally, this technique is very sensitive to humidity as in atmospheric conditions a thin water film forms on the surface of the sample. Its thickness can vary with conditions in the room, for this reason non-contact mode is usually reserved for UHV environments. 
 
 \paragraph{Tapping}
-Tapping mode is a hybrid of both contact and non-contact modes. It is also sometimes called semi contact mode. Here the tip is oscillated near the resonance frequency, but closer than in non-contact mode. The oscillation is affected by both the attractive and the repulsive part of the tip-surface potential. At the lower part of this oscillation, the tip contacts the surface. The feedback loop is the same as in non-contact mode. Due to the closer distance to the sample's surface however, the resolution is higher and a transparency with regard to thin films on the samples surface is achieved. But the tip's lifespan is reduced, due to the tapping contacting the surface. It is however much longer, than that of contact mode and damage to the sample is minimal. In this thesis, only the tapping mode of the AFM is used. As analysis was performed under atmospheric conditions.
+%Tapping mode is a hybrid of both contact and non-contact modes. 
+is also sometimes called semi contact mode. Here the tip is oscillated near the resonance frequency, but closer than in non-contact mode. The oscillation is affected by both the attractive and the repulsive part of the tip-surface potential. At the lower part of this oscillation, the tip contacts the surface. The feedback loop is the same as in non-contact mode. Due to the closer distance to the sample's surface however, the resolution is higher and a transparency with regard to thin films on the samples surface is achieved. But the tip's lifespan is reduced, due to the tapping contacting the surface. It is however much longer, than that of contact mode and damage to the sample is minimal. In this thesis, only the tapping mode of the AFM is used. As analysis was performed under atmospheric conditions.
 
 There are more ways to get useful sample information from an AFM. The tip can, for example be alloy in a magnetic coating for Magnetic Force Microscopy. For the purposes of this thesis other uses will be neglected.
 
 AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a sample's surface. Atomic force microscopy is a commonly used tool to characterize nano-lithography samples and has been extensively used in physics, material science and biology among others~\cite{afm_physics, afm_bio}.
 
+\todo{Check this again}
+
 \subsection{Scanning Electron Microscopy} 
 A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) provides images of the topography of a sample via a focused electron beam. The sample is hit by a focused beam of electrons, while suspended in vacuum. 
 
@@ -150,14 +121,14 @@ A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) provides images
 	\caption{}
 	\label{fig:sem_setup_interaction}
 	\end{subfigure}
-    \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref{fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite{SEM_image_01} and ~\cite{SEM_image_02}.}
+    \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). The three detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref{fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite{SEM_image_01} and ~\cite{SEM_image_02}.}
     \label{fig:sem_setup}
 \end{figure}
 
 The electron beam of an SEM is created using an electron gun. Often tungsten electron guns are used for their comparatively low cost and reliability. Another possibility is a \textbf{F}ield \textbf{E}mission \textbf{E}lectron \textbf{G}un (FEEG)~\cite{SEM_book}. The beam is focused using electron lenses. Accurate focusing of the electron beam is one of the major difficulties of SEM design, and spatial resolution is usually dominated by optical artifacts from the beam focus. In principle, electron lenses can use either electrostatic or magnetic fields. In practice only magnetic lenses are used since they provide less lensing abberations. Multiple sets of lenses are used to focus the beam onto the sample~\cite{SEM_book}. The different sets of lenses used to direct the beam to the sample can be seen in Figure \ref{fig:sem_setup_beam}. Due to the use of electromagnets for lensing the parameters can be controlled relatively easily. The control is partially automatic and partially done manually. \\
 
 When an electron hits the surface of the sample, the electron can undergo various interactions with the sample (Fig. \ref{fig:sem_setup_interaction}).
-The main matter interaction that is measured in an SEM is the inelastic scattering of beam electrons with sample electrons. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron~\cite{SEM_book}. Secondary electrons are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator. It converts the attracted electrons into photons, which are then detected via \textbf{P}hoto \textbf{M}ultiplier \textbf{T}ube (PMT). Such a detector is called \textbf{E}verhart–\textbf{T}hornley (ET) detector~\cite{SEM_book}. The amount of sencodary electrons detected is based on the surface's topography. Thus by measuring the voltage given at the PMT, a topographical image of the sample can be obtained. The detection of secondary electrons, back-scattered electrons and X-rays can be seen in Figure \ref{fig:sem_setup_beam}. \\
+The main matter interaction that is measured in an SEM is the inelastic scattering of beam electrons with sample electrons. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron~\cite{SEM_book}. Secondary electrons are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator. It converts the attracted electrons into photons, which are then detected via \textbf{P}hoto \textbf{M}ultiplier \textbf{T}ube (PMT). Such a detector is called \textbf{E}verhart–\textbf{T}hornley (ET) detector~\cite{SEM_book}. The amount of secondary electrons detected is based on the surface's topography. Thus by measuring the voltage given at the PMT, a topographical image of the sample can be obtained. The detection of secondary electrons, back-scattered electrons and X-rays can be seen in Figure \ref{fig:sem_setup_beam}. \\
 
 SEMs give high contrast large area images with good spatial resolution. They were used in this thesis to initially locate evaporated fields on silicon samples. SEM imaging comes with some downsides.
 On insulating or semiconducting samples, the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. To avoid this, the electron beam has to be operated at low beam energy. In theory this limits the spatial resolution as higher energy electron have a smaller De-Broglie wavelength $\alpha$, but optical effects arising from focusing the electron beam bottleneck the resolution. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference, and thus they are not sufficient for sample characterization. \\
diff --git a/chap02.aux b/chap02.aux
index 70fa20b50988381ce6fcd4aa9660e1304a328ab4..458b4055e14cc1a19c66cf048640d573324c906f 100644
--- a/chap02.aux
+++ b/chap02.aux
@@ -33,8 +33,8 @@
 \newlabel{sub@fig:calibration_uhv_points_of_interest_z1}{{a}{22}{\relax }{figure.caption.21}{}}
 \newlabel{fig:calibration_uhv_points_of_interest_z2z3}{{2.6b}{22}{\relax }{figure.caption.21}{}}
 \newlabel{sub@fig:calibration_uhv_points_of_interest_z2z3}{{b}{22}{\relax }{figure.caption.21}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.6}{\ignorespaces Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination.}}{22}{figure.caption.21}\protected@file@percent }
-\newlabel{fig:calibration_uhv_points_of_interest}{{2.6}{22}{Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination}{figure.caption.21}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.6}{\ignorespaces Points of interest for the calibration of the step size of the three piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination.}}{22}{figure.caption.21}\protected@file@percent }
+\newlabel{fig:calibration_uhv_points_of_interest}{{2.6}{22}{Points of interest for the calibration of the step size of the three piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination}{figure.caption.21}{}}
 \newlabel{fig:calibration_uhv_example_driving_z1}{{2.7a}{23}{\relax }{figure.caption.22}{}}
 \newlabel{sub@fig:calibration_uhv_example_driving_z1}{{a}{23}{\relax }{figure.caption.22}{}}
 \newlabel{fig:calibration_uhv_example_driving_z2}{{2.7b}{23}{\relax }{figure.caption.22}{}}
@@ -45,58 +45,57 @@
 \newlabel{fig:calibration_screw_diff_explain}{{2.8}{24}{Top view of the Mask Aligner with the motors Z1-Z3 and the screws on the mask frame displayed. The triangle and line construction shows the derivation for the motor movement from screw movement}{figure.caption.23}{}}
 \@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}}{24}{figure.caption.24}\protected@file@percent }
 \newlabel{fig:calibration_example}{{2.9}{24}{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit}{figure.caption.24}{}}
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+\newlabel{fig:calibration_voltage}{{2.10}{25}{Step size as a function of voltage (DC peak) with linear fit and resulting slopes marked}{figure.caption.25}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.3}Optical alignment}{25}{subsection.2.3.3}\protected@file@percent }
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+\newlabel{sub@fig:camera_alignment_example_low}{{a}{26}{\relax }{figure.caption.26}{}}
+\newlabel{fig:camera_alignment_example_high}{{2.11b}{26}{\relax }{figure.caption.26}{}}
+\newlabel{sub@fig:camera_alignment_example_high}{{b}{26}{\relax }{figure.caption.26}{}}
+\newlabel{fig:camera_alignment_example_good}{{2.11c}{26}{\relax }{figure.caption.26}{}}
+\newlabel{sub@fig:camera_alignment_example_good}{{c}{26}{\relax }{figure.caption.26}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment. }}{26}{figure.caption.26}\protected@file@percent }
+\newlabel{fig:camera_alignment_example}{{2.11}{26}{Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment}{figure.caption.26}{}}
+\newlabel{fig:optical_approach_a}{{2.12a}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:optical_approach_a}{{a}{26}{\relax }{figure.caption.27}{}}
+\newlabel{fig:optical_approach_b}{{2.12b}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:optical_approach_b}{{b}{26}{\relax }{figure.caption.27}{}}
+\newlabel{fig:optical_approach_c}{{2.12c}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:optical_approach_c}{{c}{26}{\relax }{figure.caption.27}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}}{26}{figure.caption.27}\protected@file@percent }
+\newlabel{fig:optical_approach}{{2.12}{26}{The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length}{figure.caption.27}{}}
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-\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_motors}{{a}{27}{\relax }{figure.caption.30}{}}
-\newlabel{fig:mask_aligner_nomenclature_capacitances_mask}{{2.13b}{27}{\relax }{figure.caption.30}{}}
-\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_mask}{{b}{27}{\relax }{figure.caption.30}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven.}}{28}{figure.caption.31}\protected@file@percent }
-\newlabel{fig:diagram_MA_circ}{{2.14}{28}{Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven}{figure.caption.31}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances_motors}{{2.13a}{27}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_motors}{{a}{27}{\relax }{figure.caption.28}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances_mask}{{2.13b}{27}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_mask}{{b}{27}{\relax }{figure.caption.28}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances}{{\caption@xref {fig:mask_aligner_nomenclature_capacitances}{ on input line 277}}{27}{Capacitive distance measurements}{figure.caption.28}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces (\subref  {fig:mask_aligner_nomenclature_capacitances_motors}) cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor {tab_red}{red} triangle) in relation to the three piezo motor stacks. (\subref  {fig:mask_aligner_nomenclature_capacitances_mask}) diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}}{27}{figure.caption.28}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven.}}{28}{figure.caption.29}\protected@file@percent }
+\newlabel{fig:diagram_MA_circ}{{2.14}{28}{Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven}{figure.caption.29}{}}
 \newlabel{eq:plate_capacitor}{{2.1}{28}{Capacitive distance measurements}{equation.2.3.1}{}}
-\newlabel{fig:approach_curve_example_cap}{{2.15a}{29}{\relax }{figure.caption.32}{}}
-\newlabel{sub@fig:approach_curve_example_cap}{{a}{29}{\relax }{figure.caption.32}{}}
-\newlabel{fig:approach_curve_example_cap_diff}{{2.15b}{29}{\relax }{figure.caption.32}{}}
-\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{29}{\relax }{figure.caption.32}{}}
-\newlabel{fig:approach_curve_example_first}{{2.15c}{29}{\relax }{figure.caption.32}{}}
-\newlabel{sub@fig:approach_curve_example_first}{{c}{29}{\relax }{figure.caption.32}{}}
-\newlabel{fig:approach_curve_example_second}{{2.15d}{29}{\relax }{figure.caption.32}{}}
-\newlabel{sub@fig:approach_curve_example_second}{{d}{29}{\relax }{figure.caption.32}{}}
-\newlabel{fig:approach_curve_example_full}{{2.15e}{29}{\relax }{figure.caption.32}{}}
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-\newlabel{fig:approach_curve_example}{{2.15}{29}{(a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample}{figure.caption.32}{}}
+\citation{Beeker}
+\newlabel{fig:approach_curve_example_cap}{{2.15a}{29}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:approach_curve_example_cap}{{a}{29}{\relax }{figure.caption.30}{}}
+\newlabel{fig:approach_curve_example_cap_diff}{{2.15b}{29}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{29}{\relax }{figure.caption.30}{}}
+\newlabel{fig:approach_curve_example_first}{{2.15c}{29}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:approach_curve_example_first}{{c}{29}{\relax }{figure.caption.30}{}}
+\newlabel{fig:approach_curve_example_second}{{2.15d}{29}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:approach_curve_example_second}{{d}{29}{\relax }{figure.caption.30}{}}
+\newlabel{fig:approach_curve_example_full}{{2.15e}{29}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:approach_curve_example_full}{{e}{29}{\relax }{figure.caption.30}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces (a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac  {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample.}}{29}{figure.caption.30}\protected@file@percent }
+\newlabel{fig:approach_curve_example}{{2.15}{29}{(a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample}{figure.caption.30}{}}
 \citation{Beeker}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.5}Reproducibility}{30}{subsection.2.3.5}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.33}\protected@file@percent }
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+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.31}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.16a}{30}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.32}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.16b}{30}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{30}{\relax }{figure.caption.32}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces (\subref  {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref  {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}}{30}{figure.caption.32}\protected@file@percent }
+\newlabel{fig:approach_replicability}{{2.16}{30}{(\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.32}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}\protected@file@percent }
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 \newlabel{sec:sample_prep}{{2.4.1}{31}{Sample preparation}{subsection.2.4.1}{}}
@@ -130,7 +129,7 @@
 \setcounter{subfigure}{2}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{3}
+\setcounter{@todonotes@numberoftodonotes}{1}
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diff --git a/chap02.tex b/chap02.tex
index 11fc2b5b42cfec9470d7b59b73f2a4ec4fd58016..b3b4b94da2137be45c3a79736eaf6558d9d76ceb 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -1,5 +1,38 @@
 % !TeX spellcheck = <en-US>
-\chapter{Mask Aligner}
+%\chapter{Mask Aligner}
+
+\section{Electron beam evaporation}
+Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique that in \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) deposits material onto a substrates surface.
+
+\begin{figure}[H]
+	\centering
+	\includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
+	\caption{Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }
+	\label{fig:e-beam_evap}
+\end{figure}
+
+The setup of an electron beam evaporator is shown in Figure \ref{fig:e-beam_evap}. The source material is placed inside a tungsten crucible as pellets of ultrapure ($>99$ \%) material.
+%The crucible is also heated during the evaporation process, in order to prevent it from being damaged, a material with a high melting point is chosen. Tungsten with a melting point of 3695 K ~\cite{Tungsten_melt} is usually chosen. 
+%Additionally, the crucible usually has to be water cooled to avoid outgassing during the evaporation process.
+
+In order to heat the source material it is hit with a high voltage electron beam ($\mathcal{O}$($1$~kV)), emitted by either an electron gun or a filament. This beam usually is focused using magnetic fields to hit the source material. Energy transfer heats the hit atoms and eventually leads to the evaporation according to its vapor pressure.\\
+
+%The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)~\cite{CASINO} so the heating occurs only very near to the source material's surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
+
+When the material's vapor pressure exceeds the surrounding environments pressure, a vapor forms. The sample is kept at a temperature much colder than the source material's temperature, due to this the material beam will condense on the substrate's surface forming a thin film. A shutter is used to control the deposition of the material.\\
+
+In order to ensure the material beam reaches the sample in a direct path, the mean free path (MFP) of a traveling particle has to be larger than the distance to the sample's surface. For this reason, high vacuum (HV) (MFP of $10$ cm to $1$ km) or ultra-high vacuum conditions (UHV) (MFP of $1$ km to $10^5$ km) are used.
+
+The deposition rate of the evaporator can be measured using a molecular flux monitor. The deposition rate of a material is described by the Hertz-Knudsen equation:
+\begin{equation}
+	\frac{dN}{A dt} = \frac{\alpha (p_\text{e} - p)}{\sqrt{2 \pi m k_\text{B} T}}
+	\label{eq:hertz_knudsen}
+\end{equation}
+
+where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$ is time, $\alpha$ is the sticking coefficient, $p$ is the gas pressure of the impinging gas, $m$ is the mass of a single particle, $k_\text{B}$ is the Boltzmann constant, $p_\text{e}$ is the vapor pressure of the material at the sample temperature and $T$ is the temperature~\cite{knudsen}. The sticking parameter of a material can be looked up in literature. With this, the total deposition rate can then be estimated. In practice since the pressure of the impinging gas is difficult to determine this is difficult to estimate, since it requires precise knowledge on the temperature of the source, that is typically not measured. Instead, usually calibration evaporations are performed for different heating powers and different times to determine the deposition rate for a given setup.
+
+Comparing e-beam evaporation with so-called sputtering of material onto a surface, it offers more controlled deposition~\cite{Vapor_depo_princ}. In sputtering, high energy particles are produced hitting the sample, which can lead to local roughening~\cite{sputter_damage}.
+In contrast to thermal evaporation, where the source is typically heated by Joule heating from a resistive current, higher temperatures are available with e-beam evaporation. This is required, e.g. for \ce{Nb}~\cite{tungsten_evaporation}.
 
 \section{Molecular beam evaporation chamber}
 \begin{figure}[H]
@@ -14,10 +47,10 @@ path from the \ce{Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. Th
     \label{fig:mask_aligner_chamber}
 \end{figure}
 
-The Mask Aligner vacuum system (Figure \ref{fig:mask_aligner_chamber}) consists of two areas that can be separated with vacuum gate valves~\cite{Mask_Aligner}. The \textbf{M}ain \textbf{C}hamber (MC), the Mask Aligner (MA) chamber, and the evaporator chamber. The second one is the \textbf{L}oad \textbf{L}ock (LL), a vacuum suitcase that is used to insert new samples and masks into the system. The system is pumped to UHV pressures by a turbomolecular pump and a prepump (rotary vane). 
+The Mask Aligner vacuum system (Figure \ref{fig:mask_aligner_chamber}) consists of two areas that can be separated with vacuum gate valves~\cite{Mask_Aligner}. The \textbf{M}ain \textbf{C}hamber (MC) with the Mask Aligner (MA) chamber, and the \ce{Pb} evaporator. The second one is the \textbf{L}oad \textbf{L}ock (LL), a vacuum suitcase that is used to insert new samples and masks into the system. The system is pumped to UHV pressures by a turbomolecular pump and a prepump (rotary vane). 
 Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure. A valve to a nitrogen bottle allows the system to be vented with an inert gas to avoid contamination.\\
 The main chamber is equipped with an Ion Getter Pump, such that the Load Lock can be separated from the turbomolecular pump, without loss of UHV conditions. The pumping system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV) (Fig. \ref{fig:mask_aligner_chamber}). Additionally, the Load Lock and the main chamber are separated by a Gate Valve. In order to detect leaks or contaminants in the vacuum system, a mass spectrometer is attached to the main chamber. \\
-The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV conditions, even while separated from the main pump loop. A garage with spaces for up to $14$ samples ($10$: $12\times12$ cm$^2$, $4$: Omicron size) is part of the Load lock. Masks require $2$ sample slots. For insertion and removal of masks and sample into the Mask Aligner, a wobble stick is attached to the Load lock chamber. The path of the wobble stick to the Mask Aligner is marked \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. \\
+The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV conditions, even while separated from the main pump loop. A garage with spaces for up to $14$ samples ($10$: $12\times12$ cm$^2$, $4$: Omicron size) is part of the Load lock. Masks occupy $2$ sample slots due to additional height. For insertion and removal of masks and sample into the Mask Aligner, a wobble stick is attached to the Load lock chamber. The path of the wobble stick to the Mask Aligner is marked \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. \\
 Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system. It is not further discussed in this thesis. \\
 
 \subsection{Lead evaporator}
@@ -56,15 +89,15 @@ beam path to the mask is displayed.}
 
 The Mask Aligner can be separated into 3 sections:
 The upper sample module (Fig. \ref{fig:mask_aligner_nomenclature_components}, A-G), the central mask module (Fig. \ref{fig:mask_aligner_nomenclature_components}, I-K) and the lower motor module (Fig. \ref{fig:mask_aligner_nomenclature_components}, L-Q). \\
-The sample module carries the sample and moves of the sample along the x direction. It contains a sliding rail (Fig. \ref{fig:mask_aligner_nomenclature_components} D) along which the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, E) can be moved. The sample holder is fixed with spring tension inside the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, G). It can be removed in-situ.  \\
+The sample module carries the sample and moves of the sample along the x direction. It contains a sliding rail (Fig. \ref{fig:mask_aligner_nomenclature_components} D) along which the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, E) can be moved. The sample holder is fixed with spring tension inside the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, G). It can be exchanged in-situ.  \\
 
 The mask module consists of the mask frame (Fig. \ref{fig:mask_aligner_nomenclature_components}, H), which holds the mask shuttle (Fig. \ref{fig:mask_aligner_nomenclature_components}, K). It also contacts the capacitance sensors on the mask using \ce{CuBe} leaf springs. The contacts are connected to shielded coaxial cables running to the vacuum feedthroughs. The shielding is ground to the Mask Aligner body (Fig. \ref{fig:mask_aligner_nomenclature_components}, Q). \\
 
-The motor module consists of $3$ piezo motors. They move the mask along the z axis via $3$ different pivot points. They are labeled Z1, Z2 and Z3 (Figure \ref{fig:mask_aligner_nomenclature_motors}). Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components}, P) that is clamped by $6$ piezo stacks made up of $4$ piezo plates ($\approx 0.4$ nF) each. Four of the stacks are glued directly to the Mask Aligner body. The last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, O). It is pressed against the sapphire prism via a \ce{CuBe} leaf spring (Fig. \ref{fig:mask_aligner_nomenclature_components}, N). The tension of the \ce{CuBe} spring can be adjusted with a screw mounted on it. This adjustment is critical for the reliable operation of the piezo motor. On top of the sapphire prism, an \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, M) is attached. It has a small groove in the center, where a neodymium magnet (Fig. \ref{fig:mask_aligner_nomenclature_components}, L) is located. It connects the motor to the mask frame, where a similar \ce{Al2O3} plate is placed. The three pivot points created by the magnets build an equilateral triangle, with the mask in the center. When only one motor moves up, the mask frame is tilted on the axis defined by the other two motors pivot points and the side of the mask moves closer to the sample. With the three motors arranged in a triangle arbitrary angles can be realized. Since the motor step size is $\approx 70$ nm the angular precision is approximately $\tan^{-1}(\frac{70 \text{ nm}}{23 \text{ mm}}) \approx 1.74 \times 10^{-4}$ degrees. \\
+The motor module consists of three piezo motors. They move the mask along the z axis via three different pivot points. They are labeled Z1, Z2 and Z3 (Figure \ref{fig:mask_aligner_nomenclature_motors}). Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components}, P) that is clamped by $6$ piezo stacks made up of $4$ piezo plates ($\approx 0.4$ nF) each. Four of the stacks are glued directly to the Mask Aligner body. The last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, O). It is pressed against the sapphire prism via a \ce{CuBe} leaf spring (Fig. \ref{fig:mask_aligner_nomenclature_components}, N). The tension of the \ce{CuBe} spring can be adjusted with a screw mounted on it. This adjustment is critical for the reliable operation of the piezo motor. On top of the sapphire prism, an \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, M) is attached. It has a small groove in the center, where a neodymium magnet (Fig. \ref{fig:mask_aligner_nomenclature_components}, L) is located. It connects the motor to the mask frame, where a similar \ce{Al2O3} plate is placed. The three pivot points created by the magnets build an equilateral triangle, with the mask in the center. When only one motor moves up, the mask frame is tilted on the axis defined by the other two motors pivot points and the side of the mask moves closer to the sample. With the three motors arranged in a triangle arbitrary angles can be realized. Since the motor step size is $\approx 70$ nm the angular precision is approximately $\tan^{-1}(\frac{70 \text{ nm}}{23 \text{ mm}}) \approx 1.74 \times 10^{-4}$ degrees. \\
 The direction is specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract (Fig. \ref{fig:mask_aligner_nomenclature_motors}).\\
 
 \section{Slip stick principle}
-In order to control the movement of the mask stage using the mask aligner, $3$ motors of $6$ piezo stacks each made up of $4$ piezo crystals are used. Piezo crystals expand/contract upon being supplied with a DC voltage. To enable the piezo crystals to move the stage, a sapphire prism is clamped between the $6$ piezo stacks. When one applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
+In order to control the movement of the mask stage using the mask aligner, three motors of six piezo stacks each made up of four piezo crystals are used. Piezo crystals expand/contract upon being supplied with a DC voltage. To enable the piezo crystals to move the stage, a sapphire prism is clamped between the six piezo stacks. When one applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
 First a slowly rising pulse is applied to the piezo moving the prism along with the piezo. This pulse is referred to as the "slow flank". Afterward, a very fast pulse ($<1$ $\mu$s) is applied, contracting the piezo back into its original position. The prism however due to inertia remains in position. This pulse is referred to as the "fast flank". When repeated, the prism can be moved. The direction depends on the voltage amplitude signal polarity. The simplest pulse shape allowing for this is the saw tooth wave, but other signal shapes that follow the principle can be used.
 
 \begin{figure}[H]
@@ -78,7 +111,7 @@ First a slowly rising pulse is applied to the piezo moving the prism along with
 \subsection{Motor screw configuration}
 
 In order to make sure the motors can all give similar step sizes, there are 3
-screws (see Figure \ref{fig:screw_firmness_screw_image}). One is located on each motor's leaf spring. They can control the amount of force the front plate applies to the prism and thus the friction between the prism and piezo stacks. In order to achieve similar step size for the $3$ motors. The step size in dependence of the screw firmness has to be determined. This is done by measuring
+screws (see Figure \ref{fig:screw_firmness_screw_image}). One is located on each motor's leaf spring. They can control the amount of force the front plate applies to the prism and thus the friction between the prism and piezo stacks. In order to achieve similar step size for the three motors. The step size in dependence of the screw firmness has to be determined. This is done by measuring
 the time it takes for a motor to travel a known distance. For example the
 distance of one solder anchor can be used as it is known
 to be $2$ mm. This gives a measurement fast and precise enough to determine a suitable number of rotations.
@@ -126,7 +159,7 @@ the prism has traveled in the image of the camera is measured. This is done with
 		\caption{}
 		\label{fig:calibration_uhv_points_of_interest_z2z3}
 	\end{subfigure}
-	\caption{Points of interest for the calibration of the step size of the 3 piezo motors in
+	\caption{Points of interest for the calibration of the step size of the three piezo motors in
 		UHV. (a) motor Z1, \textcolor{tab_red}{red:} top of sapphire prism, \textcolor{tab_green}{green:} end of top plate used for step size determination (b)
 		motors Z2/Z3, \textcolor{tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor{tab_green}{green:} lines used for step size determination.}
 	\label{fig:calibration_uhv_points_of_interest}
@@ -173,7 +206,6 @@ With this one gets that for each unit of distance the motor moves, the screws mo
 	\caption{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref{fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}
 	\label{fig:calibration_example}
 \end{figure}
-\todo{This graphic necessary?}
 
 A linear fit is performed for the given data. The slope gives the step size. Results are shown in Figure \ref{fig:calibration_example}. After each set of steps it has to be ensured, that the mask frame is not tilted. Excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. The \ce{Nd} magnets should not detach from the frame. Moreover, the sapphire prism can fall out of the motor if it is driven too far down. The measurement has to be done for both driving directions separately, since the step sizes will be different. Indeed, in Fig. \ref{fig:calibration_example} shows that the positive retract direction has consistently larger step sizes. The Z3 motor also shows a larger difference in step size for approach and retract than the other $2$ motors.
 
@@ -191,12 +223,11 @@ seen in Figure \ref{fig:calibration_voltage}
 The behavior is linear in the voltage, but the slope is slightly different for
 each motor. An optimum, where all motors drive similarly is at $80$ V. Also noticeable is a strong difference in slope for
 Z3. Z3 is much more influenced by voltage than the other motors, where the
-step size/V is larger by $\approx 0.3$. Variations in motor behavior can be compensated using this data. To do this different voltages would have to be applied to each channel. However, the current setup does not allow for this. Due to this new driving electronics are required.\\
+step size/V is larger by $\approx 0.3$. This calibration is used to compensate motor step size variations to avoid tilting. For this different voltage pulses need to be applied to the difference motor channels. The electronics required for this are discussed further in Chapter \ref{sec:walker}.\\
 
 \subsection{Optical alignment}
-To align mask and sample one starts optically down to a precision of $50$ $\mu$m. The capacitance sensors provide only
-small signals, at large distances. \\
-The sample has to be aligned so that its surface normal
+The capacitance sensors cannot be used for alignement when the mask sample distance is very large, since the signal is noise dominated at that point. Therefore one starts by aligning optically, down to the optical limit ($25$ $\mu$m) of this setup. \\
+To do that the sample has to be aligned so that its surface normal
 is perpendicular to the camera's view direction. No sample surface can be
 seen in camera view. No upwards tilt can be observed when viewing the side
 edge of the sample, and the upper side of the sample holder, cannot be observed. \\
@@ -228,11 +259,9 @@ placed or angled too low, (b) too high and (c) placed in good alignment. }
     \label{fig:camera_alignment_example}
 \end{figure}
 
+To measure length scales the Bresser MikroCamLab software is used. To calibrate the length scale of the software the sample ($5940 \pm 20 $ $\mu$m) is chosen.
 
-When the camera is aligned with the sample, the mask can be moved close to
-the sample. A visible gap must remain between sample and mask (Fig. \ref{fig:optical_approach_a}). Then the mask is moved toward the sample until only a five pixel gap remains (Fig. \ref{fig:optical_approach}\subref{fig:optical_approach_b}, \subref{fig:optical_approach_c}). The length of the gap can
-be optically estimated using the Bresser software. Direct contact of the sample has to be avoided at this stage. This might require retraction and subsequent approach since the motors are not located directly beneath the mask. To calibrate the length scale of the camera the sample ($5940 \pm 20 $ $\mu$m) is chosen.
-In camera view direction, the mask and sample should now be aligned within
+After the camera alignment the mask is moved close to the sample until a small gap remains. Then any mask sample tilt is corrected iteratively (Fig. \ref{fig:optical_approach_a}). Then the mask is moved toward the sample until only a five pixel gap remains (Fig. \ref{fig:optical_approach}\subref{fig:optical_approach_b}, \subref{fig:optical_approach_c}).  Direct contact of the sample has to be avoided at this stage. In camera view direction, the mask and sample should now be aligned within
 achievable optical accuracy.
  
 \begin{figure}[H]
@@ -255,17 +284,16 @@ achievable optical accuracy.
 	\caption{The progression of optical alignment up from $65 \pm 5$ $\mu$m (a) to $25 \pm 5$ $\mu$m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}
     \label{fig:optical_approach}
 \end{figure}
-\todo{Is this image clear? How do I make it more clear?}
 
 
 \newpage
 \subsection{Capacitive distance measurements}
 
-After optical alignment, the mask is further aligned to the sample via capacitive measurement. The 3
-capacitive sensors on the mask are setup to correspond with the $3$ motors (Fig. \ref{fig:mask_aligner_nomenclature_capacitances_motors}). They are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_motors}. 
+The mask is aligned to the sample via capacitive measurement. The three
+capacitive sensors on the mask are setup to correspond with the three motors (Fig. \ref{fig:mask_aligner_nomenclature_capacitances_motors}). They are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_motors}. 
 \footnote{Note that this is not true for all masks. Some of the ones provided are assembled incorrectly.}
 The masks used were created in Canada by the company Norcada.
-Each mask consist of a $200$ $\mu$m thick \ce{Si} body. A $100\times100$ $\mu$m \ce{SiN} membrane, with circular $3$ $\mu$m diameter holes, $10$ $\mu$m apart from each other, is situated in the center. The \ce{SiN} covers the whole mask and is $1$ $\mu$m thick. Below the center of the mask a trench is carved in the \ce{Si}. Around the hole membrane are $3$ gold pads, that function as capacitive sensors. The \ce{Au} of the gold pads is placed below an insulating $\approx 100$ nm layer of \ce{SiO2} at the bottom of a trench in the \ce{Si} body. They are at a distance of $0.7$ mm from the hole membrane and are located in an equilateral triangle around it. The dimensions of the mask and the capacitive sensors on the mask can be seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}.
+Each mask consist of a $200$ $\mu$m thick \ce{Si} body. A $100\times100$ $\mu$m \ce{SiN} membrane, with circular $3$ $\mu$m diameter holes, $10$ $\mu$m apart from each other, is situated in the center. The \ce{SiN} covers the whole mask and is $1$ $\mu$m thick. Below the center of the mask a trench is carved in the \ce{Si}. Around the hole membrane are three gold pads, that function as capacitive sensors. The \ce{Au} of the gold pads is placed below an insulating $\approx 100$ nm layer of \ce{SiO2} at the bottom of a trench in the \ce{Si} body. They are at a distance of $0.7$ mm from the hole membrane and are located in an equilateral triangle around it. The dimensions of the mask and the capacitive sensors on the mask can be seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}.
 
 \begin{figure}[H]
     \centering
@@ -280,7 +308,7 @@ Each mask consist of a $200$ $\mu$m thick \ce{Si} body. A $100\times100$ $\mu$m
 		\label{fig:mask_aligner_nomenclature_capacitances_mask}
 	\end{subfigure}
 	\label{fig:mask_aligner_nomenclature_capacitances}
-	\caption{(\subref{fig:mask_aligner_nomenclature_capacitances_motors}) cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor{tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref{fig:mask_aligner_nomenclature_capacitances_mask}) diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}
+	\caption{(\subref{fig:mask_aligner_nomenclature_capacitances_motors}) cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor{tab_red}{red} triangle) in relation to the three piezo motor stacks. (\subref{fig:mask_aligner_nomenclature_capacitances_mask}) diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}
 \end{figure}
 
 The readout of the capacitance sensors is carried out with a Lock-in amplifier. The piezo motors are controlled with pulses from the RHK piezo motor controller. Communication with both the RHK and the Lock-in amplifier is done with a Matlab script. Figure \ref{fig:diagram_MA_circ} shows a diagram of the communication circuit. Settings of the Lock-in amplifier are available in Appendix \ref{app:lock_in}.
@@ -292,27 +320,23 @@ The readout of the capacitance sensors is carried out with a Lock-in amplifier.
     \label{fig:diagram_MA_circ}
 \end{figure}
 
-The capacitance of each of the $3$ sensors can be approximated using a simple
+The capacitance of each of the three sensors can be approximated using a parallel
 plate capacitor model. The gold pad is one plate of the capacitor and the
 overlap of its bounds with the \ce{Si} sample can be seen as the other plate of
 the capacitor:
 \begin{equation}
-	C = \epsilon_0 \epsilon_r(r) \frac{A}{r}
+	C = \epsilon_0 (\frac{A}{r} + \epsilon_{r, \text{\ce{SiN}}} \frac{A}{r_{\text{\ce{SiN}}}} + \epsilon_{r, \text{\ce{SiO2}}} \frac{A}{r_{\text{\ce{SiO2}}}})
 	\label{eq:plate_capacitor}
 \end{equation}
-where $C$ is the capacitance, $\epsilon_0$ is the vacuum permittivity, $\epsilon_r$ is the relative permittivity between the capacitor plates, $A$ is
-the area of the gold pad and $r$ is the distance between the gold pad and the
-\ce{Si} of the sample. $r$ is both the distance of $1$ $\mu$m of \ce{SiN} on the mask's surface and the mask sample distance in vacuum. \\ 
-The capacitance increases with a $\frac{1}{r}$ dependence. This holds true until
+where $C$ is the capacitance, $\epsilon_0$ is the vacuum permittivity, $\epsilon_r$ is the relative permittivity of the corresponding material, $A$ is
+the area of the gold pad and $r$ is the distance between the mask surface and the sample. $r_{\text{\ce{SiN}}}$ and $r_{\text{\ce{SiO2}}}$ $ $
+are the thickness of the \ce{SiN} and \ce{SiO2} layers above the gold pad. This holds true until
 the mask's surface gets in contact with the sample. Contamination particles can also cause indirect contact of mask and sample.
-
-The distance to the
-sample can in theory be read off from the capacitance value via Eq.
+The distance to the sample can in theory be read off from the capacitance value via Eq.
 \ref{eq:plate_capacitor}. However, with real masks the capacitance values can
-deviate drastically from the model. Without any point of
-reference, no assessment of the absolute distance can be made.
-For this reason, a calibration curve is required to determine distances. This requires contacting the sample at
-least once. \\
+deviate drastically from the model. Without a point of
+reference, no assessment of the absolute distance can be made. A measurement of the capacitance while bringing the mask into contact with the sample and subsequent retraction are used as this reference.
+
 
 \begin{figure}[H]
     \centering
@@ -351,16 +375,13 @@ where the mask is touching the sample.}
     \label{fig:approach_curve_example}
 \end{figure}
 
-The curve obtained from approaching the sample is called an approach curve. An
-example is shown in Figure \ref{fig:approach_curve_example_cap}. The corresponding
-curve for retraction is called a retract curve. \\
+A typical approach curve, from a measured distance of $25 \pm 5$ $\mu$m to full contact is shown in Figure \ref{fig:approach_curve_example_cap}. \\
 
 Usually the mask will start contacting the sample with one point (or potentially an edge) first. An illustration of
-this is shown in Figure \ref{fig:approach_curve_example_first}. This inhibits
-the movement of the mask on the associated motor. This results in a changed
-step size. Since all motors move the mask frame this will affect all motors step sizes, albeit to different degrees. Due to
-this step size change, the slope of the approach curve changes. 
-If the sample is now contacted with an edge the step size decreases again. This is labeled in Figure
+this is shown in Figure \ref{fig:approach_curve_example_first}. The first contact inhibits
+the movement of the mask on the associated motor, resulting in a changed
+step size. Due to this step size change, the slope of the approach curve changes. 
+If the mask contacts the sample with another point (Figure \ref{fig:approach_curve_example_second}) the step size decreases again. This is labeled in Figure
 \ref{fig:approach_curve_example_cap} as "Second contact". If the sample is
 approached further, the only axis of movement left for the mask is the one
 aligning the mask to the sample perfectly (Figure
@@ -369,7 +390,7 @@ longer changes since the distance between mask and sample can no longer be
 decreased. This point is labeled "Full contact" in Figure
 \ref{fig:approach_curve_example_cap}. \\
 
-The difference in capacitance increases monotonically. When the step size changes the difference makes a sudden drop. This means the $dC$ curve gives a local maximum before each contact. This can be used to define a stop condition. A value near the peak is determined in a calibration measurement to full contact. When this value is reached in any subsequent approach the approach is stopped. How close the value can be chosen to the peak depends on the noise of the signal. \\
+The difference in capacitance increases monotonically. Upon any contact the step size changes and the $dC$ curve gives a local maximum. This can be used to define a stop condition. A value $5-10$ steps before the peak~\cite{Beeker} is determined in a calibration measurement to full contact. When this value is reached in any subsequent approach the approach is stopped. How close the value can be chosen to the peak depends on the noise of the signal. \\
 %Another way of looking at this is to consider the differences between $2$ capacitance values:
 %\begin{equation}
 %	C_2 - C_1 = \epsilon_0 \epsilon_r \frac{A}{r + r'} - \epsilon_0 \epsilon_r
@@ -405,7 +426,7 @@ and a comparison before and after evaporation were discussed~\cite{Beeker}.
 
 \subsubsection{Reproducibility when removing sample/mask}
 
-One question concerning reproducibility is whether the approach curve is strongly affected by the exchange of mask or sample, or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the production of patterned samples. 
+One question concerning reproducibility is whether the approach curve is strongly affected by the exchange of mask or sample, or even just the reinsertion of mask or sample. This can be used to perform a calibration approach curve on one sample and exchange the sample for another. This potentially allows for the evaporation on samples, which were never put into contact with a mask.
 
 \begin{figure}[H]
     \centering
@@ -423,7 +444,7 @@ One question concerning reproducibility is whether the approach curve is strongl
     \label{fig:approach_replicability}
 \end{figure} 
 
-Reinserting the mask, the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed by better gold pin design.
+Reinserting the mask, the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}.
 
 Another reason might be small movement of the mask frame on the \ce{Nd} magnets tilting the mask. This problem cannot be fixed without a complete redesign of the Mask Aligner. \\
 
@@ -615,18 +636,17 @@ Reinserting the sample also induced a difference in approach curves, but this di
 \section{Mask Aligner operation}
 
 \subsection{Sample preparation} \label{sec:sample_prep}
-The evaporation of a superconductor onto any material requires a clean sample surface. In this thesis, only \ce{Si} samples were used. To clean a \ce{Si} sample, the following steps have to be taken:
+The evaporation of a superconductor onto any material requires a clean sample surface. To clean a \ce{Si}(111) sample, the following steps have to be taken:
 
 \begin{enumerate}
-	\item Select chips from a \ce{Si} wafer and place them into a petri dish. Clean the preti dish
+	\item Select chips from a \ce{Si} wafer and place them into a petri dish. Clean the chip
 using acetone and then IPA in an ultrasonic bath.
 	\item Carefully grab a silicon chip with a soft tip tweezer and while
 maintaining stable grip, carefully blow any coarse particles from the surface of the
 chip using pressurized nitrogen. Do not blow the nitrogen at the surface, but
 across it, as otherwise the chip will just fall from the tweezer. Do this for every chip.
-	\item Place the chips in a beaker filled with pure acetone and put it in an
-ultrasonic bath. Heat the acetone using the heating function of the ultrasonic
-bath for 10 minutes, ensuring however that $55^\circ$ C are never exceeded.
+	\item Place the chips in a beaker filled pure acetone and put it in an
+ultrasonic bath. Use the ultrasonic bath for 10 minutes heated to $55^\circ$ C.
 	\item Take the chips out of the acetone with a soft tip tweezer and rinse them with IPA. Then submerge them in a beaker filled with IPA and clean them again in the ultrasonic bath for 10 minutes. No heating required.
 	\item Take the chip out again and repeat the last step with demineralized water. While waiting, combine the hardener and resin of the 2 part epoxy EPO-TEK E4110-LV to ensure it is ready for a later step.
 	\item Take the chip out and blow it dry with pressurized nitrogen, following the same procedure as step 2.
diff --git a/chap03.aux b/chap03.aux
index 72a115cba7e7e2171e88d54b4b7815e1012aa24f..412beefa7805d0f0a077aa8c0db1fff4e8ce9fb5 100644
--- a/chap03.aux
+++ b/chap03.aux
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+\newlabel{fig:diagram_MA_circ_walker}{{4.9}{71}{Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order}{figure.caption.75}{}}
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diff --git a/chap03.tex b/chap03.tex
index c4b7f8b66cae364813944357081cfc6e8f815d0a..b69f104648b971e1365a6c4848a8ce561d5e6776 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -2,7 +2,7 @@
 \chapter{Electronics}
 \section{RHK piezo motor controller}
 \subsection{Overview}
-The PMC100 Piezo motor controller by RHK technologies is a piezo motor controller designed for operating nanoscale motion in Scanning Probe systems. The piezo motor controller is capable of sending signals to $9$ separate motors at the same time. For each of these nine channels and for both direction, there are $3$ parameters that can be changed:
+The PMC100 Piezo motor controller by RHK technologies is designed for operating piezo motors for use in nanoscale systems. The piezo motor controller is capable of sending a signal to $9$ separate motors. The following parameters of the pulses can be changed for both approach and retract independently:
 \paragraph{amplitude}
 The amplitude is the peak voltage of the pulse, given in V. The default voltage for the mask aligner setup is $80$ V.
 \paragraph{sweep period}
@@ -86,12 +86,12 @@ The signal drifts (within a few $100$ steps) back to a voltage of approx. $118$
 
 Due to the aforementioned behaviors of the KIM001 device, the device was found to be incapable of providing driving pulses for the Mask Aligner and was thus deprecated.
 
-\section{Mask Aligner controller "Walker"}
+\section{Mask Aligner controller "Walker"} \label{sec:walker}
 \subsection{Overview}
 In order to find a suitable replacement for the RHK Piezo Motor controller, a new device to drive control pulses to the piezo stacks in the mask aligner was built. The \textbf{P}rinted \textbf{C}ircuit \textbf{B}oard (PCB) is based on the piezo Walker electronics designed to control the piezo Walker used for STM control. Due to this, the device is often referred to as the "Mask Aligner Walker", even though it is not a walker or stepper motor controller. Adaptations were made to adjust it to the desired slip-stick behavior needed for application in the mask aligner. The Controller takes a serial input command and then drives sinusoidal steps with a sharp fast flank at the center of the period. Controllable are the amplitude of the signal and the number of steps. A simplified overview of the entire signal generation process is shown in Appendix \ref{app:walker_diagram}. The following section will look at each part of the process in detail.
 
 \subsection{Signal generation}
-The core of the Mask aligner controller is an Arduino DUE~\cite{arduino_datasheet}. The  \textbf{C}entral \textbf{P}rocessing \textbf{U}nit (CPU) of the Arduino DUE the "Atmel SAM3X8E ARM Cortex-M3 CPU" is a $32$-Bit ARM-Core microcontroller. Integrated into the CPU is a $12$-Bit \textbf{D}igital to \textbf{A}nalog \textbf{C}onverter (DAC)~\cite{arduino_cpu_datasheet}. The DAC comes with two output channels that can output simultaneously. The signal provided to the DAC is generated via software. The Arduino generates a signal internally with a sampling rate of $404$ kHz with the shape given by:
+The core of the Mask aligner controller is an Arduino DUE~\cite{arduino_datasheet}. The  \textbf{C}entral \textbf{P}rocessing \textbf{U}nit (CPU) of the Arduino DUE the "Atmel SAM3X8E ARM Cortex-M3 CPU" is a $32$-Bit ARM-Core microcontroller. Integrated into the CPU is a $12$-Bit \textbf{D}igital to \textbf{A}nalog \textbf{C}onverter (DAC)~\cite{arduino_cpu_datasheet}. The DAC comes with two output channels that can output simultaneously. The signal provided to the DAC is generated via software. It is further discussed in Section \ref{sec:software} The Arduino generates a signal internally with a sampling rate of $404$ kHz with the shape given by:
 \begin{equation}
      S = 4095 * \frac{A}{2 \pi} * \sin(2 \pi * t/P) + t/P
 \end{equation}
@@ -115,7 +115,6 @@ The Signal given by the Arduino contains aliasing artifacts from the digital to
     \caption{(a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear. }
     \label{fig:bessel_filter}
 \end{figure}
-\todo{Aliases Signal}
 
 \subsection{Fast flank}
 
@@ -142,15 +141,15 @@ The final step is amplification since the Arduino DUE can only output voltages b
 The Arduino digital output pins $22$, $24$, $26$ and $28$ control, which channels receive any output signal. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
 Afterward there are $4$ relays, one for each channel that can be shut to prevent any current from being on the output leads, this is mainly a safety measure. The $4$ relays are also controlled by the Arduino from the digital outputs $53$, $51$, $49$ and $47$ for the channels Z1, Z2, Z3 and X respectively. The relays are switched off after a waiting period of $2$ seconds after no signal is supplied to the given channel. 
 
-\subsection{Programming}
-The software used by the Arduino to generate the signal was written in the course of this thesis. It is written in the Arduino's programming language. The software is controlled via commands send over a serial interface. \todo{What should I write with regard to the programming?}
+\subsection{Programming} \label{sec:software}
+The software used by the Arduino to generate the signal was written in the course of this thesis. It is written in the Arduino's programming language. Its source code can be found in Appendix \ref{sec:walker_code}. The software is controlled via commands sent over a serial interface. 
 
 \subsubsection{Parameters}
 The following parameters can be controlled via the new software:
 \paragraph{Amplitude (amp)}
 The amplitude of the generated signal within the Arduino given as $4095 * \text{amp} / 100$. An amplitude of $100$ results in a signal of $240$ V peak to peak at the output. To derive peak to peak voltage from this multiply by $2.4$.
 \paragraph{Voltage (volt)}
-Alternatively to setting amp, the voltage can be set directly. Internally, this sets the amp parameter. Due to limited integer precision in the amp parameter, not all voltages can be accurately chosen. The script will choose the closest voltage to the input one. The range is $0$ - $120$ V. The default value is $80$ V. 
+Alternatively to setting amp, the voltage can be set directly. Internally, this sets the amp parameter. Due to limited integer precision in the amp parameter, not all voltages can be accurately chosen. Error is $<0.5$ \%. The range is $0$ - $120$ V. The default value is $80$ V. 
 \paragraph{Channel}
 Used to specify which output channels are turned off/on. All channels receive the same signal when turned on. The system can output 4 channels of signal, where each can be turned off separately. 
 \paragraph{Max Step}
@@ -162,7 +161,7 @@ The frequency is not adjustable as of the writing of this thesis, though in prin
 
 \subsection{Measured pulse shape}
 In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed. For the Mask Aligner a voltage of $80$ V was determined to be the optimum voltage to run experiments (see point of intercept in Figure \ref{fig:calibration_voltage}), for this reason the comparisons will be made at $80$ V, unless specified otherwise. \\
-A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}).  The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walker's pulse. The Walker compares favorably to the RHK. It has a more consistent peak shape and its peak voltage corresponds to the one given as a parameter more closely than the RHK. It both under- and overshoots the specified $80$ V, by up to $\approx20$ V. The walker pulses are also more symmetric around the fast flank than the one from the RHK. Both the Walker and the RHK show no aliasing artifacts. Steps visible in Figure \ref{fig:walker_pulse_shape_slow} are due to the limited resolution of the oscilloscope (see Fig. \ref{fig:walker_pulse_shape_fast}). Given this data the Walker seems to outperform the RHK in the unloaded state and should give the same, or a better driving behavior than the RHK.
+A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}).  The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walker's pulse. The Walker compares favorably to the RHK. It has a more consistent peak shape and its peak voltage corresponds to the one given as a parameter more closely than the RHK. The RHK both under- and overshoots the specified $80$ V, by up to $\approx20$ V. The walker pulses are also more symmetric around the fast flank than the one from the RHK. Both the Walker and the RHK show no aliasing artifacts. Steps visible in Figure \ref{fig:walker_pulse_shape_slow} are due to the limited resolution of the oscilloscope (see Fig. \ref{fig:walker_pulse_shape_fast}). Given this data the Walker seems to outperform the RHK in the unloaded state.
 
 \begin{figure}[H]
     \centering
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index 0a90286c52d846f139de8d75441a349e1753c3b4..0f0260fc9f03c6c0bf4e839693da09d12985d8f2 100644
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+\newlabel{sec:piezo_reglue}{{2.4}{37}{Piezo regluing}{section.2.4}{}}
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+\newlabel{sub@fig:Z3_reglue_process_off}{{a}{37}{\relax }{figure.caption.36}{}}
+\newlabel{fig:Z3_reglue_process_scratched}{{2.4b}{37}{\relax }{figure.caption.36}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.4}{\ignorespaces The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing.}}{37}{figure.caption.36}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{2.4}{37}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing}{figure.caption.36}{}}
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+\newlabel{fig:Z3_after reglue}{{2.5}{38}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.37}{}}
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 \citation{Olschewski}
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-\newlabel{sub@fig:Front_plate_repair_tool}{{a}{51}{\relax }{figure.caption.62}{}}
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-\newlabel{fig:Feedthrough_Repairs}{{4.10}{53}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.64}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{40}{figure.caption.39}\protected@file@percent }
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+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{41}{\relax }{figure.caption.40}{}}
+\newlabel{fig:Front_plate_repair_plate}{{2.8b}{41}{\relax }{figure.caption.40}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{41}{\relax }{figure.caption.40}{}}
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+\newlabel{fig:Feedthrough_Repairs_right}{{2.10b}{43}{\relax }{figure.caption.42}{}}
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+\newlabel{fig:Feedthrough_Repairs}{{2.10}{43}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.42}{}}
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+\newlabel{fig:calibration_after_repair}{{2.11}{44}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.44}{}}
 \@setckpt{chap04}{
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+\setcounter{page}{45}
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@@ -89,7 +89,7 @@
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diff --git a/chap04.tex b/chap04.tex
index 357a636e90ddd25ff8d93b253e04c4a1321d163c..5f181276c2244c6abd1e3e4e2e79711bdf0aa478 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -20,7 +20,7 @@ The Mask Aligner was built in 2015, during the master thesis of Tim Olscchewski~
     \label{fig:Repair_Diagram}
 \end{figure}
 
-The nomenclature for the piezo motors used in the following is described in Figure \ref{fig:Repair_Diagram_diagram}. It shows  for the different parts of a single motor. Figure \ref{fig:Repair_Diagram_image} shows a photo with a similar configuration as the diagram to make clear what it corresponds to.
+The nomenclature for the piezo motors used in the following is described in Figure \ref{fig:Repair_Diagram_diagram}. It shows the different parts of a single piezo motor. Figure \ref{fig:Repair_Diagram_image} shows a photo with a similar configuration.
 
 \section{General UHV device preparation}
 %\subsection{Adding components}
@@ -36,9 +36,9 @@ The nomenclature for the piezo motors used in the following is described in Figu
 %Only materials that have been cleared for use in UHV environments should be used. Especially materials that leave residues, like adhesive tapes, should be chosen with this in mind. 
 
 \subsection{UHV compatible Soldering}
-When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments, should be used. The soldering irons for UHV use should never be used with non-UHV solder. This means that no solder containing lead can be used. \\
+When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments, should be used. \\
 Since flux can splash when heated, surrounding components have to be shielded.
-The uses flux has to be cleaned off thoroughly to avoid outgassing as well as short-circuiting from stray flux. The following steps have to be followed:
+The used flux has to be cleaned off to avoid outgassing as well as short-circuiting from stray flux. The following steps have to be followed:
 \begin{enumerate}
 	\item Using laboratory cleaning swabs and demineralized water mixed with laboratory detergent the surface that was solder on should be cleaned thoroughly, but carefully. After cleaning with the laboratory swab, rinse the surface.
 	\item The previous step should be repeated with demineralized water without any detergent
diff --git a/chap05.aux b/chap05.aux
index 0b1e645c707cc6859088865c240d40c1145f176f..b387bad07df6ed7da5e2ad45ab5b379a97409109 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,98 +1,97 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{55}{chapter.5}\protected@file@percent }
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-\newlabel{tab:evaporation_settings}{{5.1}{56}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.68}{}}
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+\newlabel{fig:evaporation_simulation_sharpness}{{3.12}{59}{(\subref {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.56}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{3.13a}{60}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{60}{\relax }{figure.caption.57}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{3.13b}{60}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{60}{\relax }{figure.caption.57}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{3.13c}{60}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{60}{\relax }{figure.caption.57}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.13}{\ignorespaces (\subref  {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref  {fig:evaporation_simulation_rejection_prev}) with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{60}{figure.caption.57}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{3.13}{60}{(\subref {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref {fig:evaporation_simulation_rejection_prev}) with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.57}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.5.3}Software improvements}{60}{subsection.3.5.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.5.4}Final Remark}{61}{subsection.3.5.4}\protected@file@percent }
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diff --git a/chap05.tex b/chap05.tex
index 4b7372545c9e333dd01a838114b48974b14d8560..72b9f3d73e2928a441790e541c2373be318e48f6 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -2,7 +2,9 @@
 \chapter{Evaporations and measurement}
 \section{Evaporation configuration}
 
-As a test for positioning and to optimize the penumbra of \ce{Pb} islands on a \ce{Si} sample, evaporations were performed on a \ce{Si} sample. The \ce{Si}(111) sample was prepared and cleaned using the process described in Section \ref{sec:sample_prep}. The Cleanliness of the sample and mask was confirmed optically before insertion into the Load Lock.
+As a test for alignment and to optimize the penumbra of \ce{Pb} islands on a \ce{Si} sample, evaporations were performed on a \ce{Si} sample. The \ce{Si}(111) sample was prepared and cleaned using the process described in Section \ref{sec:sample_prep}. The cleanliness of the sample and mask was confirmed optically before insertion into the Load Lock. Five evaporations were performed to determine edge sharpness of evaporated dots at different distances.
+
+Measurements were started at a distance of $25 \pm 5$ $\mu$m from the sample. The approach curve to full contact was recorded and the first evporation was performed in this full contact. The approach curve is shown in Figure \ref{fig:evaporation_approach_curve}.
 
 \begin{figure}[H]
     \centering
@@ -11,9 +13,9 @@ As a test for positioning and to optimize the penumbra of \ce{Pb} islands on a \
     \label{fig:evaporation_approach_curve}
 \end{figure}
 
-The 3 capacitance sensors appear heavily correlated (Fig. \ref{fig:evaporation_approach_curve}) and the uncertainty on C2 and C3 is an order of magnitude larger than the step in $dC$. For this reason C1 was primarily used for alignment. C2 and C3 were recorded but went unused.
+The 3 capacitance sensors appear heavily correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the step in $dC$. For this reason C1 was primarily used for alignment. C2 and C3 were recorded but went unused. The other evaporations were performed by retracting the mask $1000$ steps and approaching. 
 
-Five subsequent evaporations were performed at different lateral positions on the sample. Each evaporation consists of a field of $9 \times 9$ $3$ $\mu$m \ce{Pb} circles, as seen previously in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}. Each field was evaporated at different mask sample distances, as described by the approach curve. The approach curve to full contact of this particular sample is shown in Figure \ref{fig:evaporation_approach_curve} for field 1.\\  
+Four subsequent evaporations were performed at different lateral positions on the sample. Each evaporation consists of a $9 \times 9$ field of $3$ $\mu$m \ce{Pb} circles, as seen previously in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}. Each field was evaporated at different mask sample distances, as described by the approach curve. The evaporations were performed with the following stop conditions: \\  
 
 \begin{itemize}
 	\item Field 1: $1$ $\mu$m distance to sample (Full contact)
@@ -23,32 +25,7 @@ Five subsequent evaporations were performed at different lateral positions on th
 	\item Field 5: $1$ $\mu$m (Full Contact)
 \end{itemize}
 
-The evaporation parameters are shown in Table \ref{tab:evaporation_settings}.
-
-\begin{table}[H]
-	\begin{tabular}{|c|c|c|c|c|c|c|}
-		\hline
-		              & Time {[}min{]} & FIL {[}A{]} & EMIS {[}mA{]} & FLUX {[}nA{]} & Press. {[}mbar{]} & T {[}°C{]} \\ \hline \hline
-		Evap. 1 & $40$             & $1.75$        & $9.1-6.9$       & $490-540$       &$5.37 \times 10^{-9}$& $24 $                  \\ \hline
-		Evap. 2 & $40$             & $1.75$        & $9.7-5.4$       & $450-530$       &$3.86 \times 10^{-9}$& $24$                   \\ \hline
-		Evap. 3 & $40$             & $1.75$        & $9.5-5.3$       & $470-520$       &$3.21 \times 10^{-9}$& $24$                   \\ \hline
-		Evap. 4 & $40$             & $1.75$        & $10.0-4.9$      & $460-510$       &$2.99 \times 10^{-9}$& $24$                   \\ \hline
-		Evap. 5 & $40$             & $1.75$        & $6.8-4.7$       & $450-500$       &$2.86 \times 10^{-9}$& $24$                   \\ \hline
-	\end{tabular}
-	\caption{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}
-	\label{tab:evaporation_settings}
-\end{table}
-%
-%\begin{figure}[H]
-%    \centering
-%    \includegraphics[width=0.8\linewidth]{img/Evaporation/MaskAlignerChamber_evap.pdf}
-%    \caption{The Mask Aligner chamber configuration during evaporation.}
-%    \label{fig:evaporation_chamber_status}
-%\end{figure}
-
-The turbomolecular pump was by mistake not turned off during evaporation. 
-
-The pressure of the main chamber before each of the evaporations was $4.5 \times 10^{-10}$ mbar. The pressure during each evaporation was recorded, except for evaporation 4, where the software crashed during saving, corrupting the file. In this case, only the highest pressure value was recorded.
+The parameters used for the evaporator are shown in Appendix \ref{app:evaporation}. The turbomolecular pump was by mistake not turned off during evaporation. \\
 
 \begin{figure}[H]
     \centering
@@ -69,7 +46,8 @@ The pressure of the main chamber before each of the evaporations was $4.5 \times
     \label{fig:Evaporation_diagramm}
 \end{figure}
 
-Figure \ref{fig:Evaporation_diagramm_sample_img} shows the positions of the evaporated fields in regard to the sample edges and each other. The fields angle was measured to be about $10^\circ$ with regard to the sample edge. This comes from a slight misalignment of the mask on the mask holder, as seen in Figure \ref{fig:Evaporation_diagramm_mask_img}.
+After each evaporation the sample was moved laterally by $5000$ steps. First in -x direction and after the third evaporation in +x direction. The positions of the final fields on the sample are shown in Figure \ref{fig:Evaporation_diagramm_sample_img}. \\
+The fields angle was measured to be about $10^\circ$ with regard to the sample edge. This comes from a slight misalignment of the mask on the mask holder, as seen in Figure \ref{fig:Evaporation_diagramm_mask_img}.
 
 \section{Contamination}
 The entire sample's surface is contaminated with small particles, which are about $\approx 50$ nm in height with a diameter on the order of $ 10$ nm. The contaminants are not visible in an optical microscope. After cleaning, the sample was only checked optically, which is why it is unknown if they were present after cleaning or were deposited afterward. 
@@ -92,7 +70,7 @@ The entire sample's surface is contaminated with small particles, which are abou
     \label{fig:evaporation_contamination}
 \end{figure}
 
-The data in Figure \ref{fig:evaporation_contamination} shows that the particles are up to $\approx 40$ nm in height and with an average height of $24 \pm 10$ nm. The particle's average width is $40 \pm 10$. Height and width were obtained by fitting flattened Gaussian functions to the particles line cuts and extracting $2\sigma$ as well as the height of the peak. The distribution of particles across the sample surface is isotropic.
+The data in Figure \ref{fig:evaporation_contamination} shows that the particles are up to $\approx 40$ nm in height and with an average height of $24 \pm 10$ nm. The particle's average width is $40 \pm 10$ nm. Height and width were obtained by fitting flattened Gaussian functions to the particles line cuts and extracting $2\sigma$ as well as the height of the peak. The distribution of particles across the sample surface is isotropic.
 
 In addition, the sample was contaminated with larger particles possibly from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during vacuum bakeout, where the system was heated to $>100$°C for several days on $2$ separate occasions. The size of these larger particles was determined to be in the order of $\mathcal{O}(100 \text{nm})$ using SEM and on the order of $\mathit{O}(10)$ $\mu$m in diameter. \\
 Since the sample was checked only optically before insertion into UHV the small particle contamination might have been overlooked. Therefore the sample should be checked for contaminations via AFM before insertion into the chamber.
@@ -118,10 +96,10 @@ In AFM measurements it becomes clear, that the dots are not entirely circular (F
     \label{fig:penumbra_tilt_sigmas_and_field_show}
 \end{figure}
 
-In order to obtain the width of the penumbra, and other characteristics of the performed evaporation, AFM measurements were performed. For all fields, at least one measurement was taken of the $4$ cardinal directions by first measuring a low resolution image of the top right of the field and then selecting $3$ dots to take higher resolution images of. One on the top, one on the right and one near the center. An example of this is shown in Figure \ref{fig:Evaporation_diagramm_field}. The dot visualized on the left of the image is near the center of the whole field, as the image shows only a partial field. The same process is repeated for the lower left of the field. The center dot is not recorded again. The chosen dots are not necessarily the ones in the middle of the $4$ cardinal directions. They are also different dots across the 5 different fields. The criterion for choice of dot was minimal amount of contamination and AFM artifacts rather than direct correspondence to direction. \\
+AFM measurements were performed to characterize the surface of the evaporated sample. Each field was studied by taking low resolution measurements of the lower left and the upper right side of the field. A few \ce{Pb} dots, representative of the edges and the center of the field were chosen for high resolution imaging. An example of this is shown in Figure \ref{fig:Evaporation_diagramm_field}. The dot visualized on the left of the image is near the center of the whole field, as the image shows only a partial field. \\
 
-The data is cleaned by masking the contamination of the \ce{Si} sample. This worked very well since the dots' height is $\approx 3$ nm, while the contamination particles are much taller ($\approx 50$ nm). The area under the mask is interpolated in order to remove most of the particles. \\
-The width of the penumbra was then obtained by getting line cuts close to the line along which the tilt of the dots points and by fitting a Gaussian falloff to the slopes of the resulting line cut. The fit function is:
+The data is filtered by masking the contamination of the \ce{Si} sample. This worked very well since the dots' height is $\approx 3$ nm, while the contamination particles are much taller ($\approx 50$ nm). The area under the mask is interpolated in order to remove most of the particles. \\
+Line cuts close to the line along which the tilt of the dots points were obtained. By fitting a Gaussian falloff to the slopes of the line cut, the penumbra width is measured. The fit function is:
 
 \begin{equation}
  f(x, b, h, \mu, \sigma_s, \sigma_l, r) = \begin{cases} 
@@ -196,7 +174,7 @@ The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) i
 
 \section{Tilt and deformation}
 
-All evaporated dots, showed signs of a tilt between mask hole and sample, even when the capacitance signal was within the full contact regime. If this was due to misalignment between the entire mask and the sample, one would expect the direction of the tilt to be uniform. The size of $\sigma_l$ would also diminish along the direction of the tilt. To determine if this was the case the direction of the angle of the major axis was measured (example Fig. \ref{fig:evaporation_tilts_example}) and recorded for all fields (Fig. \ref{fig:evaporation_tilts_all}). As shown in Figure \ref{fig:evaporation_tilts_all} the direction of the tilt is not uniform and instead seems to point outwards for dots on the edge. This suggests the mask itself is slightly bent towards the edges, resulting in an alignment error. \\
+All evaporated dots, showed elongation of the circle, even when the mask was in full contact with the sample. If this was due to misalignment between the entire mask and the sample, one would expect the direction of the tilt to be uniform. The size of $\sigma_l$ would also diminish along the direction of the tilt. To determine if this was the case the direction of the angle of the major axis was measured (example Fig. \ref{fig:evaporation_tilts_example}) and recorded for all fields (Fig. \ref{fig:evaporation_tilts_all}). As shown in Figure \ref{fig:evaporation_tilts_all} the direction of the tilt points outwards for dots on the edge. This suggests the mask itself is bent towards the edges. \\
 
 \begin{figure}[H]
     \centering
@@ -218,47 +196,54 @@ The smallest minor axis found in the AFM data was $2.15 \pm 0.08$ $\mu$m compare
 
 \begin{figure}[H]
     \centering
-	\begin{subfigure}{0.49\linewidth}
-		\centering
-    	\includegraphics[width=0.95\linewidth]{img/Evaporation/SEM/SEM_Probe_01_cropped.png}
-    	\caption{}
-		\label{fig:evaporation_SEM_sample}
-	\end{subfigure}
-	\begin{subfigure}{0.49\linewidth}
-		\centering
+    \begin{subfigure}{0.49\linewidth}
+    	\centering
     	\includegraphics[width=0.95\linewidth]{img/Evaporation/SEM/SEM_Mask_cropped.pdf}
     	\caption{}
-		\label{fig:evaporation_SEM_mask}
-	\end{subfigure}
-	\caption{(\subref{fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref{fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}
+    	\label{fig:evaporation_SEM_mask}
+    \end{subfigure}
+    \begin{subfigure}{0.49\linewidth}
+    	\centering
+    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/ShowingClog.pdf}
+    	\caption{}
+    	\label{fig:evaporation_SEM_analysis_clog}
+    \end{subfigure}
+
+	\caption{(\subref{fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. (\subref{fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes.}
     \label{fig:evaporation_SEM}
 \end{figure}
 
-To check whether the Mask was undamaged during the evaporation, SEM images were taken of the mask as well as the sample. The resulting images can be seen in Figure \ref{fig:evaporation_SEM}. The evaporation of field $2$ shown in Figure \ref{fig:evaporation_SEM_sample} shows the elliptical tilt also visible in the AFM images. The elliptical part of the dot shows different value in the SEM image, which is an indicator, that the conductivity is different for that part of the dot. \\
+To check whether the Mask was undamaged during the evaporation, the mask was examined via SEM. The resulting images can be seen in Figure \ref{fig:evaporation_SEM}. 
+
 The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to the mask. The white areas are charging artifacts and were not stable in multiple images. The mask appears to be bending. This is not a real deformation, but the result of charging artifacts and an inherent fish-eye effect of SEM images at high magnification. 
 
 \begin{figure}[H]
     \centering
+	
 	\begin{subfigure}{0.49\linewidth}
 		\centering
-    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/ShowingClog.pdf}
+    	\includegraphics[width=0.965\linewidth]{img/Evaporation/SEM/SEM_CloggingOverlay.png}
     	\caption{}
-		\label{fig:evaporation_SEM_analysis_clog}
+		\label{fig:evaporation_SEM_analysis_clog_overlay}
 	\end{subfigure}
 	\begin{subfigure}{0.49\linewidth}
 		\centering
-    	\includegraphics[width=0.965\linewidth]{img/Evaporation/SEM/SEM_CloggingOverlay.png}
-    	\caption{}
-		\label{fig:evaporation_SEM_analysis_clog_overlay}
+		\includegraphics[width=0.95\linewidth]{img/Evaporation/SEM/SEM_Probe_01_cropped.png}
+		\caption{}
+		\label{fig:evaporation_SEM_sample}
 	\end{subfigure}
-	\caption{(\subref{fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. (\subref{fig:evaporation_SEM_analysis_clog_overlay}) tilt direction from \ref{fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}
+	
+	\caption{(\subref{fig:evaporation_SEM_analysis_clog_overlay}) tilt direction from \ref{fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields. (\subref{fig:evaporation_SEM_sample}) SEM images of field 2 on the sample.}
     \label{fig:evaporation_SEM_analysis}
 \end{figure}
 
 An example of this clogging in the SEM image is shown in Figure \ref{fig:evaporation_SEM_analysis_clog}
 To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also points outwards. For a lot of points the clogging is not clearly visible in the image however, so that no strong conclusion can be drawn from the SEM image alone. \\
 
-This data suggests multiple possible hypothesis for this elliptical dot shape. It could be that the mask deformed during evaporation or is permanently deformed. Additionally, a displacement of the mask due to vibration could cause elliptical artifacts.
+The evaporation of field $2$ shown in Figure \ref{fig:evaporation_SEM_sample} shows the elliptical tilt also visible in the AFM images. The elliptical part of the dot shows different value in the SEM image, which is an indicator, that the conductivity is different for that part of the dot. \\
+
+This data suggests multiple possible hypothesis for this elliptical dot shape. It could be that the mask deformed during evaporation or is permanently deformed. Additionally, a displacement of the mask due to vibration could cause elliptical artifacts. 
+Similar effects were previously observed, when turbo pumps were in operation during evaporation~\cite{Simon}
 
 
 \section{Simulation} \label{sec:simulation}
@@ -389,4 +374,4 @@ Godot uses its own units for length measurement, which are stored as $32$-bit fl
 
 \subsection{Final Remark}
 
-The results of the simulation show that a x-y-z vibration with a component of "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM, and that its peak to peak amplitude is within the expected range for this system. It shows that the sharper penumbra edge ($\approx 60$ nm) is the penumbra that one would obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp interfaces. \\
\ No newline at end of file
+The results of the simulation show that a x-y-z vibrational displacement with a component of vibrational "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM, and that its peak to peak amplitude is within the expected range for this system. It shows that the sharper penumbra edge ($\approx 60$ nm) is the penumbra that one would obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp edges. \\
\ No newline at end of file
diff --git a/conclusion.aux b/conclusion.aux
index 0888a35ae355a25370f8e35f3b4924bee59bcb85..2966cb08be6f87e5cf85df8bed1fcf1129bd4f0d 100644
--- a/conclusion.aux
+++ b/conclusion.aux
@@ -1,9 +1,9 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
 \citation{self_epitaxy}
-\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.81}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{72}{chapter*.76}\protected@file@percent }
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diff --git a/conclusion.tex b/conclusion.tex
index b01dcc90e8343d8470b76720b79005cba5f2a467..06694b592bb1714c64f9a05dbc6cc186cf6ef946 100644
--- a/conclusion.tex
+++ b/conclusion.tex
@@ -2,11 +2,9 @@
 \addcontentsline{toc}{chapter}{Conclusions and Outlook}
 In this thesis, the function of a mask aligner operating in UHV was optimized and its capabilities were analyzed. 
 
-Mask Aligner functionality was restored and measures were taken to prevent further failure. 
-Maintenance procedures for certain potential faults of the Mask Aligner system were established and applied to the Mask Aligner.
-Potential sources of cross capacitances on the Mask Aligner were investigated. Likely candidates for sources of cross capacitance were found on the Mask holders/shuttles. The Mask Aligner itself found to be negligible in the creation of cross capacitance. \\
+Mask Aligner functionality was restored and measures were taken to prevent further failure. \\
 
-Further research is needed on the prevention of faults in the mask preparation procedure, as issues with leakage currents, created in the process of mask bonding, were found to be the likely reason for large correlations in the capacitance signals. \\
+Further research is needed on the prevention of faults in the mask preparation procedure, created in the process of mask bonding, were found to be the likely reason for large correlations in the capacitance signals. \\
 
 A new controller for the Mask Aligner was created by the electronics workshop. Programming of the new electronic was done, and initial performance tests showed favorable results over the old driver electronics. The new controller still suffers from hardware issues, which is why tests under load could not be performed. A final performance test with calibration is still pending. \\
 
diff --git a/img/Plots/Filtering.pdf b/img/Plots/Filtering.pdf
index df54d0890fe783666091f45ddeabf08d3b5cb888..31440e72df1bcaa78a14a991b530040336f2c533 100644
Binary files a/img/Plots/Filtering.pdf and b/img/Plots/Filtering.pdf differ
diff --git a/img/Plots/FilteringDone.pdf b/img/Plots/FilteringDone.pdf
index e9286b93ab789a20164955b99e9d2a92c056614e..0bd5e4a48db1981bc4d57fed2fe48724d14177ee 100644
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diff --git a/preface.tex b/preface.tex
index 9de7de1474e9edb2a37c101a2d160c49d0689957..fd81f0c7c201ba5243f285461aaed10c8781581e 100644
--- a/preface.tex
+++ b/preface.tex
@@ -1,6 +1,6 @@
 \chapter*{Introduction}
 \addcontentsline{toc}{chapter}{Introduction}
-In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing. One problem, that is highly sought after in quantum computing, is the creation of Majorana Zero Modes, as these could potentially provide a stable and controllable way to encode information. \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes (MZM) are quasi particles that behave like Majorana fermions with non-Abelian statistics. MZMs are predicted to emerge at the core of vortices at superconductor/topological insulator interfaces~\cite{majorana_zero_modes}. These interfaces require pristine conditions and at the same time patterns, smaller than the coherence length ($<100$ nm) of the superconductor. \\
+In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing. The creation of Majorana Zero Modes is highly sought after in quantum computing, as these could potentially provide a stable and controllable way to encode information. \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes (MZM) are quasi particles that behave like Majorana fermions with non-Abelian statistics. MZMs are predicted to emerge at the core of vortices at superconductor/topological insulator interfaces~\cite{majorana_zero_modes}. These interfaces require pristine conditions and sharp ($<100$ nm) patterns of the superconductor. \\
 
 Atmospheric conditions typically deteriorate surface properties of the required samples. Due to this \textbf{U}ltra \textbf{H}igh \textbf{V}accuum (UHV) conditions are required for the sample. This often limits the pattern creation process, as exposure to ambient conditions or other chemicals are required. \\
 
@@ -9,6 +9,6 @@ Many methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography (EBL) or
 Other methods of patterning superconductors on topological insulators have been proposed, but many have shortcomings that make their use impractical. There are for example scanning probe approaches,~\cite{afm_pattern} which can directly manipulate single atoms on surfaces, but require 
 long timescales and expensive equipment. Additionally, many Scanning Probe approaches still require resists, leading to the same issues as previously mentioned.\\
 
-A simple and inexpensive approach is stencil lithography employing \textbf{P}hysical \textbf{V}apor \\ \textbf{D}eposition (PVD), where a stencil (mask) is used to mask a section of the sample. When the sample is hit with a molecular vapor beam, the masked areas are protected from the impinging material and stay pristine, while the ones not protected built patterned structures. In this method, no resist is required, and the procedure can be performed at UHV conditions. Resolutions of sub-$50$ nm have been achieved~\cite{stencil_resolution}. \\
-Stencil lithography however has its downsides. In order to get very high resolution, the mask and the sample have to be very close as otherwise the aperture of the mask creates a "penumbra", limiting the lateral resolution of the pattern. The simple and often used approach is to simply bring mask and sample into direct mechanical contact, ensuring minimal distance. This however can contaminate the sample or even mechanically damage it.\\
-To avoid this a Mask Aligner operating in UHV, the subject of this work, was designed~\cite{Olschewski, Bhaskar}. It uses capacitive measurement to ensure minimal mask sample distance during PVD, while avoiding full contact with the sample, thus preserving surface condition. This work concerns the optimization, improvement and analysis of the Mask Aligner, as well as work on the creation of additional electronics and software to drive the Mask Aligners operation. 
\ No newline at end of file
+A simple and inexpensive approach is stencil lithography employing \textbf{P}hysical \textbf{V}apor \\ \textbf{D}eposition (PVD), where a stencil (mask) is used to mask a section of the sample. When the sample is hit with a molecular vapor beam, the masked areas are protected from the impinging material and stay pristine, while the ones not protected create patterned structures. In this method, no resist is required, and the procedure can be performed at UHV conditions. Resolutions of sub-$50$ nm have been achieved~\cite{stencil_resolution}. \\
+Stencil lithography however has its downsides. In order to get very high resolution, the mask and the sample have to be very close as otherwise the aperture of the mask creates a "penumbra", limiting the sharpness of the pattern. The simple and often used approach is to simply bring mask and sample into direct mechanical contact, ensuring minimal distance. This however can contaminate the sample or even mechanically damage it.\\
+To avoid this a Mask Aligner operating in UHV, the subject of this work, was designed~\cite{Olschewski, Bhaskar}. It uses capacitive measurement to ensure minimal mask sample distance during PVD, while avoiding full contact with the sample, thus preserving surface condition. This work concerns the optimization, improvement and analysis of the Mask Aligner, as well as work on the implementation of alternative electronics and software to drive the Mask Aligner's operation. 
\ No newline at end of file
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diff --git a/thesis.bbl b/thesis.bbl
index 1a7e0f51260497aa2c75213ea12a79198c05f114..d7f67acea2dad8cf91ff636eb2d187f771ff20f6 100644
--- a/thesis.bbl
+++ b/thesis.bbl
@@ -169,6 +169,11 @@ I.~Agilent~Technologies, ``Torr seal data sheet,''
   \url{https://www.agilent.com/cs/library/datasheets/public/data-sheet-torr-seal-products-5994-5102-en-agilent.pdf},
   2022, [Accessed 02-10-2024].
 
+\bibitem{Simon}
+S.~Mathioudakis, ``{I}nbetriebnahme und {T}est eines {M}ask {A}ligners für
+  {U}ltrahochvakuum,'' Aachen, 2015, unpublished, but viewable on the Server of
+  the 2nd institute of physics B.
+
 \bibitem{grain_growth}
 \BIBentryALTinterwordspacing
 E.~BAUER, ``Phänomenologische theorie der kristallabscheidung an oberflächen.
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+++ b/thesis.blg
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 --line 96 of file bibliography.bib
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 --line 325 of file bibliography.bib
+Warning--entry type for "Simon" isn't style-file defined
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diff --git a/thesis.log b/thesis.log
index 72c62a9fb289b8d7ffcbd7a3b97ccf97373f897d..331abe937ee8caaf9621e04e7517b559d9b5a8a4 100644
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diff --git a/thesis.pdf b/thesis.pdf
index 68bcb9938753636e941d32bbd2f69ddec7d09208..7eb34a43e95b610f6850d5b2d9f83c98bb18c7a3 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index ae1568e20ba1ff6b57e0bb054144394a5909550f..545f87617dac6c87ca2a84a6ba8846322374d650 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.tex b/thesis.tex
index 27cf2049343a401bc26a55f836a5bf324a74c47d..ba18a5d49e8105b8e3f480baa575d867a86c3b3c 100644
--- a/thesis.tex
+++ b/thesis.tex
@@ -128,10 +128,11 @@
 \include{preface}
 %\include{chap00}
 \include{chap01}
-\include{chap02}
-\include{chap03}
+%\include{chap02}
+%\include{chap03}
 \include{chap04}
 \include{chap05}
+\include{chap03}
 
 \include{conclusion}
 %%% Bibliography
diff --git a/thesis.toc b/thesis.toc
index 89cf4d3aab50af33bc8e30e469639257ff7443ee..33414d75c2e3b5f9b1033631d9de7cf8864f813c 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -1,113 +1,114 @@
 \contentsline {chapter}{Introduction}{3}{chapter*.2}%
 \contentsline {chapter}{\numberline {1}Mask Aligner background}{5}{chapter.1}%
-\contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}%
-\contentsline {section}{\numberline {1.2}Stencil lithography}{6}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{7}{section*.5}%
-\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.7}%
-\contentsline {section}{\numberline {1.3}Measurement techniques}{9}{section.1.3}%
-\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{9}{subsection.1.3.1}%
-\contentsline {subsubsection}{Modes}{10}{section*.10}%
-\contentsline {paragraph}{Contact}{11}{section*.12}%
-\contentsline {paragraph}{Non-Contact}{11}{section*.13}%
-\contentsline {paragraph}{Tapping}{12}{section*.14}%
-\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{12}{subsection.1.3.2}%
-\contentsline {chapter}{\numberline {2}Mask Aligner}{15}{chapter.2}%
-\contentsline {section}{\numberline {2.1}Molecular beam evaporation chamber}{15}{section.2.1}%
-\contentsline {subsection}{\numberline {2.1.1}Lead evaporator}{16}{subsection.2.1.1}%
-\contentsline {section}{\numberline {2.2}Slip stick principle}{19}{section.2.2}%
-\contentsline {section}{\numberline {2.3}Shadow mask alignment}{20}{section.2.3}%
-\contentsline {subsection}{\numberline {2.3.1}Motor screw configuration}{20}{subsection.2.3.1}%
-\contentsline {subsection}{\numberline {2.3.2}Motor calibration}{21}{subsection.2.3.2}%
-\contentsline {subsection}{\numberline {2.3.3}Optical alignment}{25}{subsection.2.3.3}%
-\contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{27}{subsection.2.3.4}%
-\contentsline {subsection}{\numberline {2.3.5}Reproducibility}{30}{subsection.2.3.5}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.33}%
-\contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}%
-\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{31}{subsection.2.4.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{33}{chapter.3}%
-\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{33}{section.3.1}%
-\contentsline {subsection}{\numberline {3.1.1}Overview}{33}{subsection.3.1.1}%
-\contentsline {paragraph}{amplitude}{33}{section*.35}%
-\contentsline {paragraph}{sweep period}{33}{section*.36}%
-\contentsline {paragraph}{time between sweeps}{33}{section*.37}%
-\contentsline {subsection}{\numberline {3.1.2}Pulse shape}{33}{subsection.3.1.2}%
-\contentsline {section}{\numberline {3.2}KIM001}{34}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{34}{subsection.3.2.1}%
-\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{34}{subsection.3.2.2}%
-\contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{35}{subsection.3.2.3}%
-\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{36}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{36}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Signal generation}{36}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Fast flank}{37}{subsection.3.3.3}%
-\contentsline {subsection}{\numberline {3.3.4}Amplification}{38}{subsection.3.3.4}%
-\contentsline {subsection}{\numberline {3.3.5}Programming}{39}{subsection.3.3.5}%
-\contentsline {subsubsection}{Parameters}{39}{section*.46}%
-\contentsline {paragraph}{Amplitude (amp)}{39}{section*.47}%
-\contentsline {paragraph}{Voltage (volt)}{39}{section*.48}%
-\contentsline {paragraph}{Channel}{39}{section*.49}%
-\contentsline {paragraph}{Max Step}{39}{section*.50}%
-\contentsline {paragraph}{Polarity}{39}{section*.51}%
-\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{39}{subsection.3.3.6}%
-\contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{41}{subsection.3.3.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{43}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{43}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{44}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}UHV compatible Soldering}{44}{subsection.4.2.1}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{44}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo regluing}{47}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{48}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{49}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{51}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{52}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{53}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{55}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{55}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{57}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{58}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt and deformation}{63}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{66}{section.5.5}%
-\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{66}{subsection.5.5.1}%
-\contentsline {subsection}{\numberline {5.5.2}Results}{68}{subsection.5.5.2}%
-\contentsline {subsection}{\numberline {5.5.3}Software improvements}{71}{subsection.5.5.3}%
-\contentsline {subsection}{\numberline {5.5.4}Final Remark}{72}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.81}%
-\contentsline {chapter}{Bibliography}{74}{chapter*.82}%
-\contentsline {chapter}{List of Abbreviations}{77}{chapter*.83}%
-\contentsline {chapter}{Appendix}{i}{chapter*.84}%
-\contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
-\contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
-\contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
-\contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
-\contentsline {paragraph}{pulse?}{vi}{section*.87}%
-\contentsline {paragraph}{pol x}{vi}{section*.88}%
-\contentsline {paragraph}{amp x}{vi}{section*.89}%
-\contentsline {paragraph}{volt x}{vi}{section*.90}%
-\contentsline {paragraph}{channel x}{vi}{section*.91}%
-\contentsline {paragraph}{maxmstep x}{vi}{section*.92}%
-\contentsline {paragraph}{step x}{vi}{section*.93}%
-\contentsline {paragraph}{mstep x}{vi}{section*.94}%
-\contentsline {paragraph}{cancel}{vii}{section*.95}%
-\contentsline {paragraph}{help}{vii}{section*.96}%
-\contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.97}%
-\contentsline {paragraph}{angle}{vii}{section*.98}%
-\contentsline {paragraph}{radius\_mask}{vii}{section*.99}%
-\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.100}%
-\contentsline {paragraph}{distance\_sample}{vii}{section*.101}%
-\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.102}%
-\contentsline {paragraph}{running\_time}{vii}{section*.103}%
-\contentsline {paragraph}{deposition\_gain}{vii}{section*.104}%
-\contentsline {paragraph}{penalize\_deposition}{vii}{section*.105}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.106}%
-\contentsline {paragraph}{oscillation\_period}{vii}{section*.107}%
-\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.108}%
-\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.109}%
-\contentsline {paragraph}{save\_intervall}{viii}{section*.110}%
-\contentsline {paragraph}{oscillation\_dir}{viii}{section*.111}%
-\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.112}%
-\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.113}%
-\contentsline {paragraph}{random\_seed}{viii}{section*.114}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.115}%
-\contentsline {paragraph}{resolution}{viii}{section*.116}%
-\contentsline {paragraph}{path}{viii}{section*.117}%
-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.118}%
+\contentsline {section}{\numberline {1.1}Stencil lithography}{5}{section.1.1}%
+\contentsline {subsubsection}{Penumbra}{5}{section*.3}%
+\contentsline {subsubsection}{Tilt induced penumbra}{7}{section*.5}%
+\contentsline {section}{\numberline {1.2}Electron beam evaporation}{7}{section.1.2}%
+\contentsline {section}{\numberline {1.3}Molecular beam evaporation chamber}{10}{section.1.3}%
+\contentsline {subsection}{\numberline {1.3.1}Lead evaporator}{11}{subsection.1.3.1}%
+\contentsline {section}{\numberline {1.4}Slip stick principle}{14}{section.1.4}%
+\contentsline {section}{\numberline {1.5}Shadow mask alignment}{15}{section.1.5}%
+\contentsline {subsection}{\numberline {1.5.1}Motor screw configuration}{15}{subsection.1.5.1}%
+\contentsline {subsection}{\numberline {1.5.2}Motor calibration}{16}{subsection.1.5.2}%
+\contentsline {subsection}{\numberline {1.5.3}Optical alignment}{20}{subsection.1.5.3}%
+\contentsline {subsection}{\numberline {1.5.4}Capacitive distance measurements}{22}{subsection.1.5.4}%
+\contentsline {subsection}{\numberline {1.5.5}Reproducibility}{25}{subsection.1.5.5}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{25}{section*.23}%
+\contentsline {section}{\numberline {1.6}Mask Aligner operation}{26}{section.1.6}%
+\contentsline {subsection}{\numberline {1.6.1}Sample preparation}{26}{subsection.1.6.1}%
+\contentsline {section}{\numberline {1.7}Measurement techniques}{27}{section.1.7}%
+\contentsline {subsection}{\numberline {1.7.1}Atomic Force Microscopy}{27}{subsection.1.7.1}%
+\contentsline {subsubsection}{Modes}{28}{section*.26}%
+\contentsline {paragraph}{Contact}{29}{section*.28}%
+\contentsline {paragraph}{Non-Contact}{29}{section*.29}%
+\contentsline {paragraph}{Tapping}{30}{section*.30}%
+\contentsline {subsection}{\numberline {1.7.2}Scanning Electron Microscopy}{30}{subsection.1.7.2}%
+\contentsline {chapter}{\numberline {2}Mask Aligner repairs and optimizations}{33}{chapter.2}%
+\contentsline {section}{\numberline {2.1}Overview}{33}{section.2.1}%
+\contentsline {section}{\numberline {2.2}General UHV device preparation}{34}{section.2.2}%
+\contentsline {subsection}{\numberline {2.2.1}UHV compatible Soldering}{34}{subsection.2.2.1}%
+\contentsline {section}{\numberline {2.3}Soldering anchors}{34}{section.2.3}%
+\contentsline {section}{\numberline {2.4}Piezo regluing}{37}{section.2.4}%
+\contentsline {section}{\numberline {2.5}Z3 motor}{38}{section.2.5}%
+\contentsline {subsection}{\numberline {2.5.1}Front plate repair}{39}{subsection.2.5.1}%
+\contentsline {subsection}{\numberline {2.5.2}Small capacitance stack}{41}{subsection.2.5.2}%
+\contentsline {section}{\numberline {2.6}Feed through cabling optimizations}{42}{section.2.6}%
+\contentsline {section}{\numberline {2.7}Final test}{43}{section.2.7}%
+\contentsline {chapter}{\numberline {3}Evaporations and measurement}{45}{chapter.3}%
+\contentsline {section}{\numberline {3.1}Evaporation configuration}{45}{section.3.1}%
+\contentsline {section}{\numberline {3.2}Contamination}{47}{section.3.2}%
+\contentsline {section}{\numberline {3.3}Penumbra}{48}{section.3.3}%
+\contentsline {section}{\numberline {3.4}Tilt and deformation}{52}{section.3.4}%
+\contentsline {section}{\numberline {3.5}Simulation}{55}{section.3.5}%
+\contentsline {subsection}{\numberline {3.5.1}Overview and principle}{55}{subsection.3.5.1}%
+\contentsline {subsection}{\numberline {3.5.2}Results}{57}{subsection.3.5.2}%
+\contentsline {subsection}{\numberline {3.5.3}Software improvements}{60}{subsection.3.5.3}%
+\contentsline {subsection}{\numberline {3.5.4}Final Remark}{61}{subsection.3.5.4}%
+\contentsline {chapter}{\numberline {4}Electronics}{62}{chapter.4}%
+\contentsline {section}{\numberline {4.1}RHK piezo motor controller}{62}{section.4.1}%
+\contentsline {subsection}{\numberline {4.1.1}Overview}{62}{subsection.4.1.1}%
+\contentsline {paragraph}{amplitude}{62}{section*.58}%
+\contentsline {paragraph}{sweep period}{62}{section*.59}%
+\contentsline {paragraph}{time between sweeps}{62}{section*.60}%
+\contentsline {subsection}{\numberline {4.1.2}Pulse shape}{62}{subsection.4.1.2}%
+\contentsline {section}{\numberline {4.2}KIM001}{63}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Overview}{63}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Pulse shape}{63}{subsection.4.2.2}%
+\contentsline {subsection}{\numberline {4.2.3}Voltage behavior}{64}{subsection.4.2.3}%
+\contentsline {section}{\numberline {4.3}Mask Aligner controller "Walker"}{65}{section.4.3}%
+\contentsline {subsection}{\numberline {4.3.1}Overview}{65}{subsection.4.3.1}%
+\contentsline {subsection}{\numberline {4.3.2}Signal generation}{65}{subsection.4.3.2}%
+\contentsline {subsection}{\numberline {4.3.3}Fast flank}{66}{subsection.4.3.3}%
+\contentsline {subsection}{\numberline {4.3.4}Amplification}{67}{subsection.4.3.4}%
+\contentsline {subsection}{\numberline {4.3.5}Programming}{68}{subsection.4.3.5}%
+\contentsline {subsubsection}{Parameters}{68}{section*.67}%
+\contentsline {paragraph}{Amplitude (amp)}{68}{section*.68}%
+\contentsline {paragraph}{Voltage (volt)}{68}{section*.69}%
+\contentsline {paragraph}{Channel}{68}{section*.70}%
+\contentsline {paragraph}{Max Step}{68}{section*.71}%
+\contentsline {paragraph}{Polarity}{68}{section*.72}%
+\contentsline {subsection}{\numberline {4.3.6}Measured pulse shape}{68}{subsection.4.3.6}%
+\contentsline {subsection}{\numberline {4.3.7}Operation with the Mask Aligner}{70}{subsection.4.3.7}%
+\contentsline {chapter}{Conclusions and Outlook}{72}{chapter*.76}%
+\contentsline {chapter}{Bibliography}{73}{chapter*.77}%
+\contentsline {chapter}{List of Abbreviations}{76}{chapter*.78}%
+\contentsline {chapter}{Appendix}{77}{chapter*.79}%
+\contentsline {section}{\numberline {A}LockIn amplifier settings}{77}{section.4.1}%
+\contentsline {section}{\numberline {B}Evaporation parameters}{77}{section.4.2}%
+\contentsline {section}{\numberline {C}Walker principle diagram}{78}{section.4.3}%
+\contentsline {section}{\numberline {D}Walker circuit diagrams}{78}{section.4.4}%
+\contentsline {section}{\numberline {E}Mask Aligner Walker Commands}{82}{section.4.5}%
+\contentsline {paragraph}{pulse?}{82}{section*.83}%
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