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Preface: This question is about a project I am working on with a professor at my university. It is NOT for a grade, but my reputation with this professor does matter. So while my success on this project is important to me, I do not see it as unfair to seek help from SO.

That said, here is a high level overview of my project. I have an atMega328 micro. I have a Microchip SST 64Mbit flash memory card. The atmega has a hardware implementation of SPI. The flash memory has a hardware implementation of SPI.

My goal is to read data from and write data to the flash chip using the atmega is SPI master mode. The memory is organized in a multiple overlay structure which is nice for erasing but for my purposes, its basically just 32,768 pages of 256 bytes each.

To write data the basic idea is I send an instruction byte, then the starting address, then the data. To read data the basic idea is that I send an instruction byte, then the starting address, then a dummy byte, and then it starts sending me data.

Here are the data sheets:

Microcontroller: http://www.atmel.com/dyn/resources/prod_documents/doc8271.pdf

Flash: http://www.sst.com/dotAsset/40498.pdf

Code:

#include <SPI.h>
#include <Peggy2.h>

#define SS_PIN  16

Peggy2 frame1;
byte toDisp = 0;
byte checker = 0;

void setup()
{
    frame1.HardwareInit();
    pinMode(SS_PIN,OUTPUT); //set pin16 to output, SS pin
    SPI.setClockDivider(SPI_CLOCK_DIV2); //set the SPI clock to f/2, fastest possible
    SPI.begin();    //SPI lib function which sets ddr for SCK and MOSI pin
                    //MISO is auto input
                    //see SPI.cpp for more info

}

void loop()
{

    if(!checker){
                enableProgramming();
        programData();
        toDisp = receiveByte(0);
        checker = 1;
        frame1.WriteRow(0,toDisp);
    }
    frame1.RefreshAll(2);

}

byte receiveByte(unsigned long startAddress)
{
    //Begin High Speed Read Instruction
    //See p. 10 of SST data sheet
    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x0B); //high speed read instruction
    SPI.transfer(0x00); //next 3 transfers are address bits A32 - A0
    SPI.transfer(0x00); //So this will read the first byte on the chip
    SPI.transfer(0x00); //last address bits
    SPI.transfer(0xFF); //dummy byte is required to start sending data back to uP
    SPI.transfer(0xFF); //I'm hoping that if I transfer a bullshit byte, the flash
                        //chip will transfer it's data to me in the same time
    digitalWrite(SS_PIN,HIGH);
    //End High Speed Read Instruction   
    return SPDR;    
}

//will perform the read instruction starting from
//startAddress and will receive numOfBytes bytes in
//succession
void receiveBytes(int numOfBytes, unsigned long startAddress)
{
    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x0B);//high speed read instruction

}

//will perform:
// 1) Chip Erase
// and loop through:
// 1) Page Program
// 2) increment Page
//until the data has finished **note this can loop and over write beginning of memory
void programData(){
    //Begin ChipErase Instruction
    //See p. 17 of SST data sheet
    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x60);//chip erase instruction
    digitalWrite(SS_PIN,HIGH);
    delay(50);//spec'd time for CE to finish
                //don't bother polling because time to program is irrelevant
    //End ChipErase Instruction

        //Begin WREN Instruction
    //See p. 18 of SST data sheet
    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x06);//write enable instruction
    digitalWrite(SS_PIN,HIGH);
    //End WREN Instruction

    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x02); //page program instruction
    SPI.transfer(0x00); //first 8 address bits
    SPI.transfer(0x00); //2nd 8 address bits
    SPI.transfer(0x00); //3rd 8 address bits
    SPI.transfer(0xAA); //10101010 is the byte I should be writing
    digitalWrite(SS_PIN,HIGH);
    delayMicroseconds(3000); //wait 3 ms for page program


    /*
    //Begin Page-Program Instruction
    //see p. 13 of SST data sheet
    byte firstAddress = 0;
    byte secondAddress = 0;
    //this loop will write to every byte in the chips memory
    //32,768 pages of 256 bytes = 8,388,608 bytes
    for(unsigned int i = 0; i < 32,768; ++i) //long variable is number of pages
    {
        digitalWrite(SS_PIN,LOW);
        ++secondAddress; //cycles from 0 to 255, counts pages
        firstAddress = i>>8; // floor(i/256)

        SPI.transfer(0x02);//Page-Program instruction byte
        SPI.transfer(firstAddress); //increments every 256 pages i.e. at page 256 this should be 1
        SPI.transfer(secondAddress); //increments every 256 bytes, i.e every page
        SPI.transfer(0x00); //beginning of a page boundary
        for(int j = 0; j < 256; ++j) //number of bytes per page
        {
            SPI.transfer(2program[(256*i) + j]);//data byte transfer            
        }
        digitalWrite(SS_PIN,HIGH);
        delayMicroseconds(2500); //2500us (2.5ms) delay for each page-program instruction to execute
    }
    //End Page-Program Instruction
    */
}

//Will prepare the chip for writing by performing:
// 1) arm the status register
// 2) Write Enable instruction
//Only needs to be performed once!
void enableProgramming(){
    //Begin EWSR & WRSR Instructions
    //See p. 20 of SST data sheet for more info
    digitalWrite(SS_PIN,LOW); //lower the SS pin
    SPI.transfer(0x50); //enable write status register instruction
    digitalWrite(SS_PIN,HIGH); //raise the SS pin
    delay(10);
    digitalWrite(SS_PIN,LOW); //lower the SS pin
    SPI.transfer(0x01); //write the status register instruction
    SPI.transfer(0x00);//value to write to register
                //xx0000xx will remove all block protection
    digitalWrite(SS_PIN,HIGH);
    //End EWSR & WRSR Instructions

    //Begin WREN Instruction
    //See p. 18 of SST data sheet
    digitalWrite(SS_PIN,LOW);
    SPI.transfer(0x06);//write enable instruction
    digitalWrite(SS_PIN,HIGH);
    //End WREN Instruction

}

So this is supposed to be a test program which programs 1 byte onto the flash and then reads it back and displays that byte on an LED array I have. If you're interested in the LED array, it can be found here: http://evilmadscience.com/tinykitlist/157

I believe my read function works because the first time I ran this, all 8 LEDs lit up. That would indicate to me that it read the flash memory when it was in it's factory state of all 1s. Now apparently I've screwed something up with the writing because the byte that lights up does not correspond at all with the byte that I'm attempting to program.

I should also note I'm using the default SPI library for arduinos and the frame buffer functions work. When I do frame1.WriteRow(toDisp), that is working correctly and has been tested extensively.

If anyone has the time or patience to figure out what I'm doing wrong that would be extremely awesome.

EDIT: To help debugging:
The LEDs are being driven by driver chips which use the SPI interface as well. I did not write that part of the code. On an oscilloscope I can see the SCK line being driven by that part of the code. However, I also have a probe on the MOSI pin and if I don't light up any lights, it never appears to go high. To me that means I'm not sending information correctly. Aka... perhaps my SPI.transfer() needs an enable function or something? Anybody have experience with this?