Java Keccak-256 implementation incorrect hash on zero byte message

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I have been trying to write my own implementation of Keccak-256 cryptographic hash function in Java. I have been using Keccak specifications summary and their Implementation Guide for reference. I want to test my implementation using a zero length input. According to this online tool. The zero length input should have a hash of: C5D2460186F7233C927E7DB2DCC703C0E500B653CA82273B7BFAD8045D85A470 but my hash is something else.

My code is located here on Github. My thoughts are that I must have done something wrong on the padding of the message(that is all that gets hashed) or something on byte order in my conversion of byte[] to longs and back, or the absorbing/squeezing phase. In my implementation I only need keccak-f[1600] which means there is only 64bits in each lane and that each block is 1088 bits or 136 bytes. I chose to use a five-by-five 2D array of longs to represent the state in my code.

Using a zero byte message means that there should only be one block of 136 bytes which should be all just padding. According to this post since keccak uses little-endian my padding should be in this order of bytes:

byte[] p = new byte[136];
p[7] = (byte) 0x01;
p[135] = (byte) 0x80;

I have looked at someone else's implementation but I can't seem to find out where my error is.

This is the sponge function:

public byte[] keccak(byte[] Mbytes, int r, int c) { // r should be 1088 and c should be 512 for Keccack-256
    // Padding
    byte[] paddedMessage = concatBytes(Mbytes, pad(r, Mbytes.length));
    System.out.println("Padded Message size: " + paddedMessage.length);

    // Initialize State
    A = new long[5][5];

    // Break up message into blocks r bits or 136 bytes
    byte[] block = new byte[136];
    int n = paddedMessage.length / block.length; // number of blocks
    System.out.println("Blocks: " + n);

    for (int i = 0; i < n; i++) { // For each block
        //set block values
        for (int j = 0; j < block.length; j++) {
            block[j] = paddedMessage[i * block.length + j];
        }
        printBlock(block);

        // Fill state
        for (int x = 0; x < 5; x++) {
            for (int y = 0; y < 5; y++) {
                int index = x + 5 * y;
                if (index < r/w) {
                    long value = decodeLELong(block, index * 8);
                    System.out.println(value + " index: " + index);
                    A[x][y] = A[x][y] ^ value;
                    A = keccakF1600(A);
                }
            }
        }
    }
    byte[] output = new byte[0]; // Size should be 256 bits/Z
    int bytesFilled = 0;
    for (int x = 0; x < 5; x++) {
        for (int y = 0; y < 5; y++) {
            int index = x+5*y;
            if (index < r/w) {
                if (bytesFilled < 136) {
                    // Take out a long from state and concat it to output.
                    output = concatBytes(output, encodeLELong(A[x][y]));
                    bytesFilled += 8;
                    A = keccakF1600(A);
                }
            }
            if (bytesFilled == 32) {
                //System.out.println("Finished Hash");
                return output;
            }
        }
    }

    return output;
}

This is my pad function:

 private byte[] pad(int x, int m) { // x/size should be 1088 or 136 bytes
    byte[] p = null;
    int q = 136 - (m % 136); // number of padding bytes
    //System.out.println("Pad q: " + q + "  m: " + m);
    if(q == 136) { // Whole block is padding
        p = new byte[136];
        p[7] = (byte) 0x01;
        p[135] = (byte) 0x80;
    }
    else { // Ignore for now
        p = new byte[q];
        p[0] = 1;
    }
    return p;
}

And this is my code for the keccak permutation:

public long[][] keccakF1600(long[][] A) { // KECCAK-f where b = 1600
    for (int i = 0; i < 24; i++) { // 24 Rounds
        A = Round1600(A, RC[i]);
    }
    return A;
}

private long[][] Round1600(long[][] A, long rc) {
    // θ Step
    long[] C = new long[5];
    for (int x = 0; x < 5; x++) {
        C[x] = A[x][0] ^ A[x][1]^ A[x][2] ^ A[x][3] ^ A[x][4];
    }

    long[] D = new long[5];
    for (int x = 0; x < 5; x++) {
        D[x] = C[(x + 4) % 5] ^ Long.rotateLeft(C[(x + 1) % 5], 1);
    }
    for (int x = 0; x < 5; x++) {
        for (int y = 0; y < 5; y++) {
            A[x][y] = A[x][y] ^ D[x];
        }
    }

    // ρ and π steps
    long[][] B = new long[5][5];
    for (int x = 0; x < 5; x++) {
        for (int y = 0; y < 5; y++) {
            B[y][(2 * x + 3 * y) % 5] = Long.rotateLeft(A[x][y], rot_offset(x,y));
        }
    }

    // χ step
    for (int x = 0; x < 5; x++) {
        for (int y = 0; y < 5; y++) {
            A[x][y] = B[x][y] ^ ((~B[(x+1) % 5][y]) & B[(x+2) % 5][y]);
        }
    }

    // ι step
    A[0][0] = A[0][0] ^ rc;

    return A;
}


private int rot_offset(int x, int y) {
    switch (x){
        case 0:
            switch (y) {
                case 0:
                    return 0;
                case 1:
                    return 36;
                case 2:
                    return 3;
                case 3:
                    return 41;
                case 4:
                    return 18;
            }
        case 1:
            switch (y) {
                case 0:
                    return 1;
                case 1:
                    return 44;
                case 2:
                    return 10;
                case 3:
                    return 45;
                case 4:
                    return 2;
            }
        case 2:
            switch (y) {
                case 0:
                    return 62;
                case 1:
                    return 6;
                case 2:
                    return 43;
                case 3:
                    return 15;
                case 4:
                    return 61;
            }
        case 3:
            switch (y) {
                case 0:
                    return 28;
                case 1:
                    return 55;
                case 2:
                    return 25;
                case 3:
                    return 21;
                case 4:
                    return 56;
            }
        case 4:
            switch (y) {
                case 0:
                    return 27;
                case 1:
                    return 20;
                case 2:
                    return 39;
                case 3:
                    return 8;
                case 4:
                    return 14;
            }
    }
    System.out.println("Should not Happen!");
    return -1; // Should not happen!
}

And finally the helper metheods to convert byte[] to long and back:

public static long decodeLELong(byte[] buf, int off)
{
    return (buf[off + 0] & 0xFFL)
            | ((buf[off + 1] & 0xFFL) << 8)
            | ((buf[off + 2] & 0xFFL) << 16)
            | ((buf[off + 3] & 0xFFL) << 24)
            | ((buf[off + 4] & 0xFFL) << 32)
            | ((buf[off + 5] & 0xFFL) << 40)
            | ((buf[off + 6] & 0xFFL) << 48)
            | ((buf[off + 7] & 0xFFL) << 56);
}
public static byte[] encodeLELong(long val)
{
    byte[] buf = new byte[8];
    buf[0] = (byte)val;
    buf[1] = (byte)(val >>> 8);
    buf[2] = (byte)(val >>> 16);
    buf[3] = (byte)(val >>> 24);
    buf[4] = (byte)(val >>> 32);
    buf[5] = (byte)(val >>> 40);
    buf[6] = (byte)(val >>> 48);
    buf[7] = (byte)(val >>> 56);
    return buf;
}

Last helper method for concatBytes:

public static byte[] concatBytes(byte[] in1, byte[] in2) {
    byte[] output = new byte[in1.length + in2.length];
    for (int i = 0; i < in1.length; i++) {
        output[i] = in1[i];
    }
    for (int i = 0; i < in2.length; i++) {
        output[i + in1.length] = in2[i];
    }
    return output;
}
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