update the testdata readme

Author: LalehB

testdata/README.md

@@ -13,7 +13,10 @@ This folder contains various subdirectories that store `.stim` files, which are
 ```
 
 ### 1. `surfacecodes/`
-This folder contains `.stim` files for surface codes, which are a family of topological quantum error-correcting codes. The filenames encode parameters such as:
+This folder contains `.stim` files for rotated surface codes. These protocols were introduced in:
+Eric Dennis, Alexei Kitaev, Andrew Landahl, John Preskill; Topological quantum memory. J. Math. Phys. 1 September 2002; 43 (9): 4452–4505. https://doi.org/10.1063/1.1499754
+
+The filenames encode parameters such as:
 - `r`: Number of rounds
 - `d`: Code distance
 - `p`: Noise probability
@@ -28,7 +31,9 @@ r=11,d=11,p=0.0001,noise=si1000,c=surface_code_X,q=241,gates=cz.stim
 ```
 
 ### 2. `colorcodes/`
-Contains `.stim` files for color codes, which are another class of topological quantum error-correcting codes. The filenames encode parameters such as:
+Contains `.stim` files for color code memory protocols. The specific syndrome extraction circuit is the 'superdense' cycle from:
+Gidney, Craig, and Cody Jones. "New circuits and an open source decoder for the color code." arXiv preprint arXiv:2312.08813 (2023).
+The filenames encode parameters such as:
 - `r`: Number of rounds
 - `d`: Code distance
 - `p`: Noise probability
@@ -43,7 +48,10 @@ r=1,d=11,p=0.01,noise=data_qubit_X,c=color_code_mpp,q=91,gates=mpp.stim
 ```
 
 ### 3. `bivariatebicyclecodes/`
-Contains `.stim` files for bivariate bicycle codes, a category of quantum error-correcting codes distinct from topological codes. These files include additional parameters related to the code structure, including:
+Contains `.stim` files for bivariate bicycle codes, as studied in:
+Bravyi, S., Cross, A.W., Gambetta, J.M. et al. High-threshold and low-overhead fault-tolerant quantum memory. Nature 627, 778–782 (2024). https://doi.org/10.1038/s41586-024-07107-7
+
+These files include additional parameters related to the code structure, including:
 - `r`: Number of rounds
 - `d`: Code distance
 - `p`: Noise probability
@@ -61,7 +69,10 @@ r=10,d=10,p=0.0001,noise=si1000,c=bivariate_bicycle_X,nkd=[[108,8,10]],q=216,isc
 ```
 
 ### 4. `surface_code_trans_cx_circuits/`
-This folder contains `.stim` files for surface code circuits that implement transversal CX (CNOT) gates. These circuits are used for fault-tolerant quantum computation and logical gate operations within surface codes. The `.stim` file naming follows the same convention as the other directories but may include CX-specific parameters.
+This folder contains `.stim` files for surface code circuits that implement transversal CX (CNOT) gates. These protocols are naturally suited for neutral atom architectures and the correlated decoding of their error models was studied in:
+Cain, Madelyn, et al. "Correlated decoding of logical algorithms with transversal gates." Physical Review Letters 133.24 (2024): 240602.
+
+The `.stim` file naming follows the same convention as the other directories but may include CX-specific parameters.
 
 Example filename:
 ```