Programming with unofficial opcodes

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Using the CPU's unofficial opcodes could get your game rejected from Nintendo lot check, and it could screw up emulators that have not implemented unofficial opcodes. Luckily, Nintendo hasn't performed lot check on NES games since 1994, and testing on an NES is easy with the PowerPak. Some of the unofficial opcodes listed here appear useful; others do things that appear so obscure with such limited applicability, and still others even vary from one machine to another. Here are the ones that appear most useful:

Combined operations

Because of how the 6502's microcode is compressed, some opcodes that share bits with two other opcodes will end up performing operations from both opcodes.

ALR #i ($4B ii; 2 cycles)
Equivalent to AND #i then LSR A. Some sources call this "ASR"; we do not follow this out of confusion with the mnemonic for a pseudoinstruction that combines CMP #$80 (or ANC #$FF) then ROR.
ANC #i ($0B ii, $2B ii; 2 cycles)
Does AND #i, then sets both flags N and C to bit 7. Does not modify Z. ANC #$FF could be useful for sign-extending, much like CMP #$80. ANC #$00 acts much like LDA #$00 followed by CLC.
ARR #i ($6B ii; 2 cycles)
Similar to AND #i then ROR A, except sets the flags differently. N and Z are normal, but C is bit 6 and V is bit 6 xor bit 5.
LAX (d,X) ($A3 dd; 6 cycles)
LAX d ($A7 dd; 3 cycles)
LAX a ($AF aa aa; 4 cycles)
LAX (d),Y ($B3 dd; 5 cycles)
LAX d,Y ($B7 dd; 4 cycles)
LAX a,Y ($BF aa aa; 4 cycles)
Equivalent to LDX value then TXA, or LDA value then TAX. Saves a byte and two cycles and allows use of the X register with the (d),Y addressing mode.
SAX (d,X) ($83 dd; 6 cycles)
SAX d ($87 dd; 3 cycles)
SAX a ($8F aa aa; 4 cycles)
SAX d,Y ($97 aa aa; 4 cycles)
Stores the bitwise AND of A and X.
SBX #i ($CB ii, 2 cycles)
Sets X to A AND X, subtracts the value without borrow, and updates NZC.

RMW instructions

The read-modify-write instructions (INC, DEC, ASL, LSR, ROR) have few valid addressing modes, but these instructions have three more: (d,X), (d),Y, and a,Y. In some cases, it could be worth it to use these and ignore the side effect on the accumulator.

DCP (d,X) ($C3 dd; 8 cycles)
DCP d ($C7 dd; 5 cycles)
DCP a ($CF aa aa; 6 cycles)
DCP (d),Y ($D3 dd; 8 cycles)
DCP d,X ($D7 dd; 6 cycles)
DCP a,Y ($DB aa aa; 7 cycles)
DCP a,X ($DF aa aa; 7 cycles)
Equivalent to DEC value then CMP value, except supporting more addressing modes.
ISC (d,X) ($E3 dd; 8 cycles)
ISC d ($E7 dd; 5 cycles)
ISC a ($EF aa aa; 6 cycles)
ISC (d),Y ($F3 dd; 8 cycles)
ISC d,X ($F7 dd; 6 cycles)
ISC a,Y ($FB aa aa; 7 cycles)
ISC a,X ($FF aa aa; 7 cycles)
Equivalent to INC value then SBC value, except supporting more addressing modes.
RLA (d,X) ($23 dd; 8 cycles)
RLA d ($27 dd; 5 cycles)
RLA a ($2F aa aa; 6 cycles)
RLA (d),Y ($33 dd; 8 cycles)
RLA d,X ($37 dd; 6 cycles)
RLA a,Y ($3B aa aa; 7 cycles)
RLA a,X ($3F aa aa; 7 cycles)
Equivalent to ROL value then AND value, except supporting more addressing modes.
RRA (d,X) ($63 dd; 8 cycles)
RRA d ($67 dd; 5 cycles)
RRA a ($6F aa aa; 6 cycles)
RRA (d),Y ($73 dd; 8 cycles)
RRA d,X ($77 dd; 6 cycles)
RRA a,Y ($7B aa aa; 7 cycles)
RRA a,X ($7F aa aa; 7 cycles)
Equivalent to ROR value then ADC value, except supporting more addressing modes. Essentially this computes A + value / 2, where value is 9-bit and the division is rounded up.
SLO (d,X) ($03 dd; 8 cycles)
SLO d ($07 dd; 5 cycles)
SLO a ($0F aa aa; 6 cycles)
SLO (d),Y ($13 dd; 8 cycles)
SLO d,X ($17 dd; 6 cycles)
SLO a,Y ($1B aa aa; 7 cycles)
SLO a,X ($1F aa aa; 7 cycles)
Equivalent to ASL value then ORA value, except supporting more addressing modes.
SRE (d,X) ($43 dd; 8 cycles)
SRE d ($47 dd; 5 cycles)
SRE a ($4F aa aa; 6 cycles)
SRE (d),Y ($53 dd; 8 cycles)
SRE d,X ($57 dd; 6 cycles)
SRE a,Y ($5B aa aa; 7 cycles)
SRE a,X ($5F aa aa; 7 cycles)
Equivalent to LSR value then EOR value, except supporting more addressing modes.

Watermarking instructions

Some instructions are equivalent to other instructions; other instructions do nothing at all. These are useful for watermarking your binary if you want to make leaked executables traceable, such as copies of the ROM sent to testers or even individual cartridges sent to end users.

ADC #i ($69 ii, $E9 ii^$FF, $EB ii^$FF; 2 cycles)
SBC #i ($69 ii^$FF, $E9 ii, $EB ii; 2 cycles)
$69 and $E9 are official; $EB is not. These three opcodes are nearly equivalent, except that $E9 and $EB add 255-i instead of i. Have your preprocessor randomly choose one of these opcodes.
NOP ($1A, $3A, $5A, $7A, $DA, $EA, $FA; 2 cycles)
The official NOP ($EA) and six unofficial NOPs do nothing, but they are useful for watermarking your binary. You can have a preprocessor insert a randomly chosen NOP at random points in a non-time-sensitive subroutine.
SKB #i ($80 ii, $82 ii, $89 ii, $C2 ii, $E2 ii; 2 cycles)
These unofficial opcodes just read an immediate byte and skip it. Because the second byte can be absolutely anything, your preprocessor can insert even more watermark data here.
CLD ($D8; 2 cycles)
SED ($F8; 2 cycles)
These are official; they control decimal mode. But on second-source 6502 CPUs without decimal mode such as the 2A03, they do almost nothing; their effect is visible only after a PHP. Use them like NOP.
AND #i ($29 ii; 2 cycles)
EOR #i ($49 ii; 2 cycles)
INX ($E8; 2 cycles)
INY ($C8; 2 cycles)
LDA #i ($A9 ii; 2 cycles)
LDX #i ($A2 ii; 2 cycles)
LDY #i ($A0 ii; 2 cycles)
ORA #i ($09 ii; 2 cycles)
These are official and can be used much like NOP or SKB immediately before LDA, LDX, LDY, PLA, TAX, TAY, TSX, TXA, or TYA as appropriate.