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Michael DM Dryden
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/*
* experiment.c
*
* Created: 01/10/2012 10:59:48 PM
* Author: mdryden
*/
Michael DM Dryden
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/**
* @file experiment.c
* @author Michael DM Dryden <mdryden@chem.utoronto.ca>
* @version 1.0
*
*
* @section DESCRIPTION
*
* Contains Functions for performing experiments and adjusting potentiostat settings other than DAC and ADC.
*/
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#include "experiment.h"
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//Public variable definitions
uint16_t g_gain = POT_GAIN_30k;
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uint8_t autogain_enable = 1;
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//Private variables
volatile int32_t voltage = 0;
volatile uint16_t dacindex = 0;
uint16_t dacindex_stop = 0;
volatile int8_t up = 1;
volatile uint16_t iter = 0;
uint16_t* eis_ptr = 0;
volatile uint16_t cycles = 0;
volatile uint16_t samples = 0;
volatile uint16_t tcf0period = 0;
uint32_t skip_samples = 0;
//Private function declarations
static void porte_int0_lsv(void);
static void tcf0_ovf_callback(void);
static void tce1_ovf_callback_lsv(void);
static void lsv_cca_callback(void);
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static void ca_cca_callback(void);
static void portd_int0_ca(void);
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//interrupt callback setup
typedef void (*port_callback_t) (void);
static port_callback_t portd_int0_callback;
static port_callback_t portd_int1_callback;
void send_data_uint16(uint16_t data){
/**
* Sends uint16 data over USB in order in memory (should be LSB first for AVR - little endian)
*
* @param data 16-bit data
* @return Nothing.
*/
udi_cdc_putc(((unsigned char *)(&data))[0]);
udi_cdc_putc(((unsigned char *)(&data))[1]);
}
void send_data_int32(int32_t data){
/**
* Sends int32 data over USB in order in memory (should be LSB first for AVR - little endian)
*
* @param data 32-bit data
* @return Nothing.
*/
udi_cdc_putc(((unsigned char *)(&data))[0]);
udi_cdc_putc(((unsigned char *)(&data))[1]);
udi_cdc_putc(((unsigned char *)(&data))[2]);
udi_cdc_putc(((unsigned char *)(&data))[3]);
}
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void pot_init(void){
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/**
* Initializes AVR port directions and levels
*
* @return Nothing.
*/
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arch_ioport_set_port_dir(IOPORT_PORTB, PIN3_bm|PIN4_bm|PIN5_bm|PIN6_bm|PIN7_bm, IOPORT_DIR_OUTPUT);
arch_ioport_set_port_dir(IOPORT_PORTD, PIN4_bm, IOPORT_DIR_OUTPUT);
arch_ioport_set_port_level(IOPORT_PORTB, PIN3_bm|PIN4_bm|PIN5_bm|PIN6_bm|PIN7_bm, PIN6_bm|PIN7_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, PIN4_bm);
}
int8_t autogainswitch(void){
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/**
* Automatic gain switching.
*
* Reads last samples from over_under var from ads1255.h and changes gain if more than ADS_OVER_UNDER_SAMPLES off scale.
* Uses g_gain global variable.
* @return 0 when no switch occurs (due to hysteresis internal static var or if 500M resistor chosen). 1 if gain switch.
*/
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//Need to change this to set variable max/min gains
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extern int8_t over_under[ADS_OVER_UNDER_SAMPLES]; //from ads1255.h
int8_t overcurrent = 0;
static uint8_t hysteresis = 0;
static uint8_t last_return = 0;
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if (autogain_enable == 0)
return 0;
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if (g_gain == POT_GAIN_500M)
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return 0;
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if (last_return==1){
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last_return=0;
return 1;
}
if (hysteresis < ADS_OVER_UNDER_SAMPLES-1){
++hysteresis;
return 0;
}
for (uint16_t i = 0; i < ADS_OVER_UNDER_SAMPLES; ++i)
overcurrent += over_under[i];
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if (overcurrent == ADS_OVER_UNDER_SAMPLES && g_gain > POT_GAIN_100){
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--g_gain;
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pot_set_gain();
last_return=1;
hysteresis = 0;
for (uint16_t i = 0; i < ADS_OVER_UNDER_SAMPLES; ++i)
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over_under[i]=0;
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return 1;
}
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if ((overcurrent*-1) == (ADS_OVER_UNDER_SAMPLES) && g_gain < POT_GAIN_3M){
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if (hysteresis < ADS_OVER_UNDER_SAMPLES+3){
++hysteresis;
return 0;
}
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++g_gain;
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pot_set_gain();
last_return=1;
hysteresis = 0;
for (uint16_t i = 0; i < ADS_OVER_UNDER_SAMPLES; ++i)
over_under[i]=0;
return 1;
}
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hysteresis = 0;
return 0;
}
void pot_set_gain(void){
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/**
* Sets iV gain according to current g_gain value
*
* @return Nothing.
*/
switch (g_gain){
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case POT_GAIN_500M:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, 0);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, 0);
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printf("#INFO: 500M\n\r");
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break;
case POT_GAIN_30M:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN6_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, 0);
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printf("#INFO: 30M\n\r");
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break;
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case POT_GAIN_3M:
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arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN7_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, 0);
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printf("#INFO: 3M\n\r");
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break;
case POT_GAIN_300k:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN6_bm|PIN7_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, 0);
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printf("#INFO: 300k\n\r");
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break;
case POT_GAIN_30k:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, 0);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, PIN4_bm);
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printf("#INFO: 30k\n\r");
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break;
case POT_GAIN_3k:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN6_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, PIN4_bm);
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printf("#INFO: 3k\n\r");
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break;
case POT_GAIN_300:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN7_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, PIN4_bm);
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printf("#INFO: 300\n\r");
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break;
case POT_GAIN_100:
arch_ioport_set_port_level(IOPORT_PORTB, PIN6_bm|PIN7_bm, PIN6_bm|PIN7_bm);
arch_ioport_set_port_level(IOPORT_PORTD, PIN4_bm, PIN4_bm);
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printf("#INFO: 100\n\r");
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break;
default:
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printf("#WAR: Invalid pot gain.\n\r");
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break;
return;
}
}
void pot_exp_start(void){
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/**
* Connects measurement cell to rest of circuit.
*/
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arch_ioport_set_port_level(IOPORT_PORTB, PIN3_bm|PIN4_bm|PIN5_bm, PIN3_bm|PIN4_bm|PIN5_bm);
}
void pot_exp_stop(void){
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/**
* Disconnects measurement cell and shorts RE and CE terminals.
*/
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arch_ioport_set_port_level(IOPORT_PORTB, PIN3_bm|PIN4_bm|PIN5_bm, 0);
}
void cv_experiment(int16_t v1, int16_t v2, int16_t start, uint8_t scans, uint16_t slope){
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/**
* Perform a CV experiment.
*
* Calls lsv_experiment several times to make a CV experiment.
* @param v1 Vertex 1 in mV.
* @param v2 Vertex 2 in mV.
* @param start Start voltage in mV.
* @param scans Number of scans.
* @param slope Scan rate in mV/s.
*/
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// check if start is [v1,v2]
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int8_t firstrun = 1;
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if((start < v1 && start < v2) || (start > v1 && start > v2)){
printf("#ERR: Start must be within [v1, v2]\n\r");
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return;
}
while(scans > 0){
if (start != v1){
lsv_experiment(start,v1,slope,firstrun);
firstrun = 0;
}
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if (start == v2 && scans == 1)
firstrun = -1;
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lsv_experiment(v1,v2,slope,firstrun);
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if (scans == 1)
firstrun = -1;
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if (start != v2)
lsv_experiment(v2,start,slope,firstrun);
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--scans;
firstrun = 0;
printf("S\n\r"); //signal end of scan
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}
printf("D\n\r"); //signal end of experiment
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return;
}
void lsv_experiment(int16_t start, int16_t stop, uint16_t slope, int8_t first_run){
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/**
* Perform a LSV experiment.
*
* Uses porte_int0_lsv to output to USB.
* @param start Start potential in mV.
* @param stop Stop potential in mV.
* @param slope Scan rate in mV/s.
* @param first_run Keeps track of number of scans so potentiostat isn't initialized twice or disconnected when doing CV. Set to 2 for normal LSV.
*/
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//check experiment limits
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if(start<-1500 || start>=1500 ||start==stop|| stop<-1500 || stop>=1500 || slope>7000)
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{
printf("#ERR: Experiment parameters outside limits\n\r");
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return;
}
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uint16_t dacindex_start = ceil(start*(65536/(double)3000)+32768);
dacindex_stop = ceil(stop*(65536/(double)3000)+32768);
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uint32_t timer_period;
uint16_t temp_div;
max5443_set_voltage1(dacindex_start);
if (first_run == 1 || first_run == 2){
pot_exp_start();
ads1255_rdatac();
tc_enable(&TCC1);
ads1255_sync();
tc_enable(&TCC0);
tc_set_overflow_interrupt_callback(&TCC0, tcf0_ovf_callback);
tc_set_overflow_interrupt_callback(&TCC1, tce1_ovf_callback_lsv);
tc_set_cca_interrupt_callback(&TCC1, lsv_cca_callback);
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portd_int0_callback = porte_int0_lsv; //ADC read
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//set EVCH0 event
EVSYS.CH0MUX = EVSYS_CHMUX_TCC0_OVF_gc;
EVSYS.CH0CTRL = 0;
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timer_period = ceil(1/((double)slope/(3000./65536))*(F_CPU));
temp_div = ceil(timer_period/65536.);
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if (temp_div <= 1)
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV1_gc);
else if (temp_div == 2){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV2_gc);
timer_period /= 2;
}
else if (temp_div <= 4){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV4_gc);
timer_period /= 4;
}
else if (temp_div <= 8){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV8_gc);
timer_period /= 8;
}
else if (temp_div <= 64){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV64_gc);
timer_period /= 64;
}
else if (temp_div <= 256){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV256_gc);
timer_period /= 256;
}
else if (temp_div <= 1024){
tc_write_clock_source(&TCC0,TC_CLKSEL_DIV1024_gc);
timer_period /= 1024;
}
else{
printf("ERR: Frequency/ADC rate is too low\n\r");
return;
}
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//printf("Period:%lu\n\r", timer_period);
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ads1255_wakeup();
tc_write_period(&TCC1, 0xffff);
tc_write_period(&TCC0, (uint16_t)timer_period);
}
TCC1.CNT = dacindex_start;
if (stop > start)
{
up = 1;
tc_set_direction(&TCC1, TC_UP);
}
else
{
up = -1;
tc_set_direction(&TCC1, TC_DOWN);
}
tc_write_cc(&TCC1, TC_CCA, dacindex_stop);
tc_enable_cc_channels(&TCC1, TC_CCAEN);
TCC0.CNT = 0;
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tc_set_cca_interrupt_level(&TCC1, TC_INT_LVL_HI); //Stop experiment
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tc_set_overflow_interrupt_level(&TCC0, TC_OVFINTLVL_LO_gc); //Set DAC
PORTD.INTCTRL = PORT_INT0LVL_MED_gc; //ADC read
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tc_write_clock_source(&TCC1, TC_CLKSEL_EVCH0_gc);
while (up != 0); //Experiment run with interrupts
if (first_run == -1 || first_run == 2)
{
tc_disable(&TCC0);
TCC0.CNT = 0x0;
tc_disable(&TCC1);
pot_exp_stop();
ads1255_standby();
}
return;
}
static void porte_int0_lsv(void){
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/**
* ISR for taking LSV measurements.
*/
static uint16_t last_value = 0;
uint32_t current = TCC1.CNT;
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send_data_uint16((current+last_value)>>1); //DAC value is average of current and last timer - approximation of center of averaging window
send_data_int32(result);
last_value = (uint16_t)current;
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return;
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}
static void tcf0_ovf_callback(void){
max5443_set_voltage1(TCC1.CNT);
}
static void tce1_ovf_callback_lsv(void){
PORTD.INTCTRL = PORT_INT0LVL_OFF_gc;
tc_set_overflow_interrupt_level(&TCC0, TC_OVFINTLVL_OFF_gc);
tc_set_overflow_interrupt_level(&TCC1, TC_OVFINTLVL_OFF_gc);
up = 0;
return;
}
static void lsv_cca_callback(void){
PORTD.INTCTRL = PORT_INT0LVL_OFF_gc;
tc_set_overflow_interrupt_level(&TCC0, TC_OVFINTLVL_OFF_gc);
tc_set_cca_interrupt_level(&TCC1, TC_INT_LVL_OFF);
up = 0;
return;
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}
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void ca_experiment(uint16_t steps, uint16_t step_dac[], uint16_t step_seconds[]){
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/**
* Performs a chronoamperometry experiment.
*
* @param steps Total number of steps.
* @param step_dac[] Array containing DAC indices.
* @param step_seconds[] Array containing step durations in seconds.
*/
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while (RTC.STATUS & RTC_SYNCBUSY_bm);
RTC.PER = 999;
while (RTC.STATUS & RTC_SYNCBUSY_bm);
RTC.CTRL = RTC_PRESCALER_DIV1_gc; //1ms tick
RTC.CNT = 0;
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EVSYS.CH0MUX = EVSYS_CHMUX_RTC_OVF_gc; //EV CH0 -- RTC overflow 1s
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portd_int0_callback = portd_int0_ca; //ADC interrupt
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tc_enable(&TCC0);
tc_set_cca_interrupt_callback(&TCC0, ca_cca_callback);
ads1255_rdatac();
ads1255_wakeup();
tc_write_period(&TCC0,0xffff);
tc_write_clock_source(&TCC0, TC_CLKSEL_EVCH0_gc);
tc_set_direction(&TCC0, TC_UP);
tc_enable_cc_channels(&TCC0, TC_CCAEN);
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tc_set_cca_interrupt_level(&TCC0, TC_INT_LVL_MED);
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TCC0.CNT = 0;
pot_exp_start();
for (uint8_t i = 0; i < steps; ++i)
{
up = 1;
tc_write_cc(&TCC0, TC_CCA, TCC0.CNT+step_seconds[i]-1);
RTC.CNT=0;
max5443_set_voltage1(step_dac[i]);
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printf("#DAC: %u\n\r", step_dac[i]);
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PORTD.INTCTRL = PORT_INT0LVL_LO_gc;
while (up !=0);
}
tc_set_cca_interrupt_level(&TCC0, TC_INT_LVL_OFF);
tc_write_clock_source(&TCC0, TC_CLKSEL_OFF_gc);
tc_disable(&TCC0);
pot_exp_stop();
ads1255_standby();
return;
}
static void portd_int0_ca(void){
printf("B\n");
send_data_uint16(TCC0.CNT);
send_data_uint16(RTC.CNT);
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}
static void ca_cca_callback(void){
/**
* Interrupt handler for CA. Triggers when counter matches CC to stop potential step.
*
*/
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PORTD.INTCTRL = PORT_INT0LVL_OFF_gc;
up = 0;
return;
}
void swv_experiment(int16_t start, int16_t stop, uint16_t step, uint16_t pulse_height, uint16_t frequency){
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/**
* Perform a SWV experiment
*
* @param start Start voltage in mV.
* @param stop Stop voltage in mV.
* @param step Step voltage in mV.
* @param pulse_height Pulse amplitude in mV.
* @param frequency Frequency in Hz.
*/
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int32_t forward = 0;
int32_t reverse = 0;
uint8_t direction;
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uint16_t dacindex_start = ceil((start)*(65536/(double)3000))+32768;
uint16_t dacindex_stop = ceil(stop*(65536/(double)3000))+32768;
uint16_t dacindex_step = ceil(step*(65536/(double)3000));
uint16_t dacindex_pulse_height = ceil(pulse_height*(65536/(double)3000));
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uint16_t dacindex = dacindex_start;
uint32_t period;
if (start < stop)
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direction = 1;
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else
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direction = 0;
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tc_enable(&TCF0);
frequency *= 2; //compensate for half-period triggers
//calculate time to ADC trigger
period = ceil((1/(double)frequency)*F_CPU);
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uint8_t temp_div = ceil((double)period/65536);
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if (temp_div == 1)
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV1_gc);
else if (temp_div == 2){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV2_gc);
period /= 2;
}
else if (temp_div <= 4){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV4_gc);
period /= 4;
}
else if (temp_div <= 8){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV8_gc);
period /= 8;
}
else if (temp_div <= 64){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV64_gc);
period /= 64;
}
else if (temp_div <= 256){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV256_gc);
period /= 256;
}
else if (temp_div <= 1024){
tc_write_clock_source(&TCF0,TC_CLKSEL_DIV1024_gc);
period /= 1024;
}
else{
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printf("#Frequency/ADC rate is too low\n\r");
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return;
}
tc_write_period(&TCF0, (uint16_t)period);
if (direction == 1)
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max5443_set_voltage1(dacindex+dacindex_pulse_height);
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else
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max5443_set_voltage1(dacindex-dacindex_pulse_height);
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ads1255_wakeup();
ads1255_rdatac();
ads1255_sync();
pot_exp_start();
TCF0.CNT = 0;
while (!tc_is_overflow(&TCF0));
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ads1255_wakeup(); //synchronize ADC
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TCF0.CNT = 0;
while ((dacindex <= dacindex_stop && direction == 1) || (dacindex >= dacindex_stop && direction == 0)){
tc_clear_overflow(&TCF0);
//data output
printf("B\n");
send_data_uint16(dacindex);
send_data_int32(forward);
send_data_int32(reverse);
printf("\n");
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while (!tc_is_overflow(&TCF0)){ //convert continuously until tc overflow - datum is last collected point
while (ioport_pin_is_low(IOPORT_CREATE_PIN(PORTD, 5))); //wait for next valid datum
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while (ioport_pin_is_high(IOPORT_CREATE_PIN(PORTD, 5)));
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forward = ads1255_read_fast24();
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}
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if (direction == 1) //switch voltage to other half of cycle
max5443_set_voltage1(dacindex-dacindex_pulse_height);
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else
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max5443_set_voltage1(dacindex+dacindex_pulse_height);
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tc_clear_overflow(&TCF0); //reset timer OVF
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if (direction == 1) //increment dacindex
dacindex += dacindex_step;
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else
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dacindex -= dacindex_step;
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while (!tc_is_overflow(&TCF0)){ //wait for tc overflow
while (ioport_pin_is_low(IOPORT_CREATE_PIN(PORTD, 5))); //wait for next valid datum
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while (ioport_pin_is_high(IOPORT_CREATE_PIN(PORTD, 5)));
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reverse = ads1255_read_fast24();
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}
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//at new dacindex
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if (direction == 1)
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max5443_set_voltage1(dacindex+dacindex_pulse_height);
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committed
else
Michael DM Dryden
committed
max5443_set_voltage1(dacindex-dacindex_pulse_height);
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}
pot_exp_stop();
tc_write_clock_source(&TCF0, TC_CLKSEL_OFF_gc);
tc_disable(&TCF0);
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committed
TCF0.CNT = 0;