File content as of revision 13:a8e096e715bd:

#include "mbed.h"
#include "SDFileSystem.h"
#include "Adafruit_ADS1015.h"
#include "MCP40D17.h"
#include "wire.h" //Used with the RTC in this code. Will need to try and remove this, and also create the correct library/update addresses and registers for the RTC.
#include "STC3100.h"
#include "LSM303.h"
#include "BME280.h"

#define SERIAL_BAUD_RATE    9600
#define SCL         20  
#define SDA         22
#define Crono       0xD0       //D0 for the chronoDot

I2C i2c(p22, p20);
Adafruit_ADS1115 ads(&i2c);
MCP40D17 DigPot(&i2c);
BME280 bmesensor(p22, p20);
STC3100 gasG(p22, p20);
Serial  pc(USBTX, USBRX);
DigitalOut blower(p29, 0);
LSM303 movementsensor(p22, p20);

//Timer t;

//float battAmps;
//float battVolts;
//float battGG;

float accel_x;
float accel_y;
float accel_z;
float mag_x;
float mag_y;
float mag_z;

int omronReading;
int vInReading;
int vBlowerReading;
int omronDiff;
int digital_pot_setpoint = 0x07; //min = 0x7F, max = 0x00
char filename[] = "/sd/UPASLOG00.txt";

TwoWire Wire = TwoWire(NRF_TWI0);    
SDFileSystem sd(SPIS_PSELMOSI, SPIS_PSELMISO, SPIS_PSELSCK, SPIS_PSELSS, "sd"); // I believe this matches Todd's pinout, let me know if this doesn't work. (p12, p13, p15, p14)

uint8_t Seconds = 0;//Seconds
uint8_t Minutes = 0;//Minutes
uint8_t Hour    = 0;//Hour
uint8_t Date    = 0;//Date
uint8_t Month   = 0;//Month
uint8_t Year    = 0;//Year
double secondsD = 0;

void get_time()
{
    Wire.beginTransmission(Crono); // address DS3231
    Wire.write(0x0E);              // select register
    Wire.write(0x1C);              // write register bitmap, bit 7 is /EOSC
    Wire.endTransmission();
    wait(0.05);
    Wire.beginTransmission(Crono);
    Wire.write(0x00);
    Wire.endTransmission();
    Wire.requestFrom(Crono+1, 7);
    
    while( Wire.available() > 0 )
    {
        Seconds = Wire.read();
        Minutes = Wire.read();
        Hour    = Wire.read();
        uint8_t day =Wire.read(); // we don't uses this, it's just day of the week
        Date    = Wire.read();
        Month   = Wire.read();
        Year    = Wire.read();
        //pc.printf("%f", sec); pc.printf("\n");//this is still in bit form
        //pc.printf("%f", min); pc.printf("\n");
        //pc.printf("%f", hr);  pc.printf("\n");
    }
    Year    = ((Year&0xF0)>>4)*10 + (Year&0x0F);           //Year
    Month   = ((Month&0x10)>>4)*10 + (Month&0x0F);         //Month
    Date    = ((Date&0x30)>>4)*10 + (Date&0x0F);           //Date
    Hour    = ((Hour&0x30)>>4)*10 + (Hour&0x0F);         //Hour
    Minutes = ((Minutes&0x70)>>4)*10 + (Minutes&0x0F);   //Minutes
    Seconds = ((Seconds&0x70)>>4)*10 + (Seconds&0x0F);   //Seconds
}
  
int main()
{

//t.start();
    // create a new file
   
   DigPot.writeRegister(digital_pot_setpoint);
   Wire.begin(SCL, SDA, TWI_FREQUENCY_100K);// 
    wait(1);
  blower = 1;
  wait (1);
    
 
  for (uint8_t i = 0; i < 100; i++) {
      filename[11] = i/10 + '0';
      filename[12] = i%10 + '0';
      FILE *fp = fopen(filename, "r");
      if (fp == NULL) {
      // only open a new file if it doesn't exist
      FILE *fp = fopen(filename, "w");
      fclose(fp);
      break;  // leave the loop!
                    } 
    }
 

         
    while(1){
     
    get_time(); 
    
    secondsD = Seconds;
    
    if(fmod(secondsD,10)==0){
    
    movementsensor.getACCEL();
    movementsensor.getCOMPASS();
    accel_x = movementsensor.AccelData.x;
    accel_y = movementsensor.AccelData.y;
    accel_z = movementsensor.AccelData.z;
    mag_x = movementsensor.MagData.x;
    mag_y = movementsensor.MagData.y;
    mag_z = movementsensor.MagData.z;
    omronReading = ads.readADC_SingleEnded(0, 0xC583); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
    //omronReading = ads.readADC_SingleEnded(0, 0xC183); // read channel 0 PGA = 1 : Full Scale Range = 4.096V
    vInReading = ads.readADC_SingleEnded(1, 0xD583); // read channel 0
    vBlowerReading = ads.readADC_SingleEnded(2, 0xE783); // read channel 0
    omronDiff = ads.readADC_Differential(0x8583); // differential channel 2-3
    //battAmps = gasG.getAmps();
    //battVolts = gasG.getVolts();
    //battGG = gasG.getCharge();
    //pc.printf("%d Amps, %d Volts, %d GG\n", gasG.getAmps(), gasG.getVolts(), gasG.getCharge());
      //Mount the filesystem
    sd.mount();
    FILE *fp = fopen(filename, "a");
    fprintf(fp, "%d,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d,%2.2f,%04.2f,%2.2f,%.0f,%.0f,%.0f,%.0f,%.0f,%.0f\r\n", Year,Month,Date,Hour,Minutes,Seconds,omronReading,vInReading, vBlowerReading, omronDiff, gasG.getAmps(), gasG.getVolts(), gasG.getCharge(), bmesensor.getTemperature(), bmesensor.getPressure(),bmesensor.getHumidity(),accel_x, accel_y, accel_z, mag_x, mag_y, mag_z);
    fclose(fp);
    //Unmount the filesystem
    sd.unmount();
    DigPot.writeRegister(digital_pot_setpoint);
   
    wait(1);
   
    }
   
    
    }
}