assuming you are using the generated sufrace code (rotated/unrotated memory), you can add a phase flip to the data qubits, ancillas, or both, by reading their indices off of where they appear in the circuit. For example, all qubits are initially reset, and all ancillas are measured during the measurement round. For example, calling stim.Circuit.generated('surface_code:rotated_memory_x', distance=3, rounds=10)
will give you, among others, the code:
RX 1 3 5 8 10 12 15 17 19
R 2 9 11 13 14 16 18 25
TICK
H 2 11 16 25
TICK
CX 2 3 16 17 11 12 15 14 10 9 19 18
TICK
CX 2 1 16 15 11 10 8 14 3 9 12 18
TICK
CX 16 10 11 5 25 19 8 9 17 18 12 13
TICK
CX 16 8 11 3 25 17 1 9 10 18 5 13
TICK
H 2 11 16 25
TICK
MR 2 9 11 13 14 16 18 25
...
from which you can read off the data qubits (RX 1 3 5 8 10 12 15 17 19
) and ancillas (MR 2 9 11 13 14 16 18 25
).
You can then add the dephasing where needed by using the object model of the circuit.