When designing a Nuclear Magnetic Resonance (NMR) DIY experiment, precise generation of pulse sequences is essential. These pulse sequences are crucial for manipulating the nuclear spins and detecting resonance signals. For such experiments, the Arduino Due is an excellent choice due to its high clock speed (84 MHz) and advanced timer capabilities, which allow for the generation of accurate timing pulses.
1. Importance of Pulse Sequence Generation in NMR
In NMR spectroscopy, pulse sequences are precisely timed RF (Radio Frequency) pulses applied to a sample to manipulate the nuclear spins of atoms. These sequences, like the 90° pulse (π/2) and 180° pulse (π), help in achieving different magnetic resonance effects necessary for analyzing molecular structures. The timing, duration, and spacing of these pulses are critical to obtaining accurate and interpretable NMR signals.
2. Leveraging the Arduino Due's Timer/Counter Hardware
The Arduino Due is equipped with multiple Timer/Counter (TC) modules, each containing several channels that can be programmed to generate precise pulse sequences:
- Frequency and Pulse Width Control: The Arduino Due's timers can be configured with different prescaler values and counter values to control the duration and timing of pulses precisely.
- Programming Flexibility: There are two primary methods to control the timers:
- Direct Register Manipulation: For more precise and advanced control.
- Using Libraries: The DueTimer library simplifies the configuration process.
3. Example: Generating Pulse Sequences Using the DueTimer Library
The DueTimer library provides a user-friendly way to configure timers on the Arduino Due. You can install the library via the Arduino IDE's Library Manager to simplify the timer setup.
Sample Code: Generating a Basic Pulse Sequence
Below is an example code that demonstrates how to generate a basic pulse sequence of a 90° pulse followed by a 180° pulse using the DueTimer library:
#include <DueTimer.h>
// Define pulse timing in microseconds
#define PULSE_90_DURATION 10 // 90-degree pulse duration (adjust as needed)
#define PULSE_180_DURATION 20 // 180-degree pulse duration (adjust as needed)
#define PULSE_INTERVAL 100 // Interval between pulses in microseconds
// Output pin for RF pulses
const int pulsePin = 7;
void setup() {
pinMode(pulsePin, OUTPUT);
// Attach Timer for 90-degree pulse
Timer1.attachInterrupt(generate90Pulse);
Timer1.start(PULSE_INTERVAL); // Set timer interval between pulses
}
void loop() {
// Nothing to do in loop, as pulses are generated in timer interrupts
}
void generate90Pulse() {
// Generate 90-degree pulse
digitalWrite(pulsePin, HIGH);
delayMicroseconds(PULSE_90_DURATION);
digitalWrite(pulsePin, LOW);
// Wait for the interval
delayMicroseconds(PULSE_INTERVAL);
// Generate 180-degree pulse
generate180Pulse();
}
void generate180Pulse() {
// Generate 180-degree pulse
digitalWrite(pulsePin, HIGH);
delayMicroseconds(PULSE_180_DURATION);
digitalWrite(pulsePin, LOW);
}
Explanation of Code:
- Timer1 is used to control the timing between the pulses.
generate90Pulse()function is called periodically by the Timer1 interrupt to produce a 90° pulse.- After generating the 90° pulse, the code waits for the defined interval and then calls
generate180Pulse()to produce the 180° pulse. delayMicroseconds()function provides the required pulse width.
4. Direct Register Manipulation Approach
If you require more precise control over the timers, you can directly manipulate the Timer/Counter (TC) registers of the Arduino Due. This requires a more in-depth understanding of the SAM3X8E microcontroller used in the Due.
- Timer/Counter Registers: The SAM3X8E has multiple Timer Counters, each capable of generating different waveforms.
- Waveform Mode: The TC modules can be set in waveform mode to produce a single pulse or a sequence of pulses.
Here is an example to generate a single pulse using Timer Counter Channel 0:
void setup() {
// Enable peripheral clock for TC0
pmc_enable_periph_clk(ID_TC0);
// Set up TC0 channel 0 for waveform generation
Tc *tc = TC0;
TcChannel *ch = &tc->TC_CHANNEL[0];
ch->TC_CMR = TC_CMR_TCCLKS_TIMER_CLOCK1 | // Use MCK/2 clock
TC_CMR_WAVE | // Enable waveform mode
TC_CMR_WAVSEL_UP_RC; // Count up to RC
ch->TC_RC = 42; // Set frequency (84MHz / 2 / 42 = 1 MHz)
ch->TC_RA = 21; // Set pulse width (50% duty cycle)
// Enable interrupt on RC compare
ch->TC_IER = TC_IER_CPCS;
ch->TC_IDR = ~TC_IER_CPCS;
// Start TC
tc->TC_CCR = TC_CCR_SWTRG | TC_CCR_CLKEN;
// Enable interrupt in NVIC
NVIC_EnableIRQ(TC0_IRQn);
}
void TC0_Handler() {
Tc *tc = TC0;
TcChannel *ch = &tc->TC_CHANNEL[0];
// Clear status register to acknowledge interrupt
ch->TC_SR;
// Toggle the pin (or do any other processing)
digitalWrite(7, !digitalRead(7));
}
void loop() {
// Main loop can be used for other tasks
}
Explanation of Direct Register Manipulation:
TC_CMR(Channel Mode Register): Configures the timer clock source, mode, and waveform options.TC_RC(Register C): Determines the frequency of the waveform.TC_RA(Register A): Determines the pulse width or duty cycle.- Interrupt Handling: The TC0_Handler() function handles the timer interrupt to toggle the output pin or perform other tasks.
5. Synchronization for Complex Pulse Sequences
For more advanced NMR experiments, you may need to generate complex pulse sequences (such as composite pulses or phase cycling) where synchronization between different pulses is essential. This can be done by:
- Combining multiple timers to generate overlapping or staggered pulses.
- Utilizing timer interrupts to coordinate actions across multiple output pins, allowing for more complex pulse patterns.
6. Conclusion
The Arduino Due is a powerful tool for generating precise pulse sequences needed for NMR spectroscopy experiments. The DueTimer library provides an easy-to-use interface for beginners, while direct register manipulation allows for advanced and precise control over pulse generation. With careful programming and understanding of pulse timing and synchronization, you can create robust and reliable pulse sequences for your NMR DIY experiments.