add contents to README

README.md

@@ -8,12 +8,30 @@ The scripts used to train and test RUDEs on shear rheometric data were developed
 
 Computational fluid dynamics simulations were performed using [OpenFOAM](https://openfoam.org/download/archive/) v9, with the [rheoTool](https://github.com/fppimenta/rheoTool) v5.0 toolbox.
 
-The scripts used to process experimental linear response data and to plot OpenFOAM simulation results were developed using [Python](https://www.python.org/downloads/) 3.8.5 with the following packages: NumPy 1.19.2, Matplotlib 3.3.2, SciPy 1.5.2, CSV 1.0, and pandas 1.1.3.
+The scripts used to process experimental linear response data and to plot OpenFOAM simulation results were developed using [Python](https://www.python.org/downloads/) 3.8.5, with the following packages: NumPy 1.19.2, Matplotlib 3.3.2, SciPy 1.5.2, CSV 1.0, and pandas 1.1.3.
 
 ## Contents
 
 ### `giesekus`
 
+- `rude.jl`: Julia script to generate synthetic shear stress LAOS data for the Giesekus model, train a RUDE using this data, and test the RUDE on shear and normal stress data in LAOS as well as shear stress data in shear startup
+- `tbnn.bson`: pre-trained model weights for a RUDE trained using the `rude.jl` script
+- `OpenFOAM`: directory containing the files needed to simulate a 4:1 contraction flow
+	- `Giesekus`: directory containing the setup files for an OpenFOAM simulation of the Giesekus model, including the mesh file (`system/blockMeshDict`), details for the integration and finite volume schemes (`system/fvSchemes` and `system/fvSolution`), definition of the constitutive model (`constant/constitutiveProperties`), and initial conditions (`0`)
+	- `Oldroyd-BLog`: directory containing the setup files for an OpenFOAM simulation of the Oldroyd-B model (defined by the log-conformation tensor). Same file structure as the `Giesekus` directory
+	- `RUDE`: directory containing the setup files for an OpenFOAM simulation of a trained RUDE. Same file structure as the `Giesekus` directory, with three additional files (`weights1.txt`, `weights2.txt`, and `weights3.txt`) containing the pre-trained weights for the TBNN layers obtained using the `rude.jl` script
+	- `simdata`: directory containing selected results from the OpenFOAM simulations, including centerline velocities, velocity profiles, the velocity field, and streamlines
+	- `make_plots.py`: Python script for plotting the simulation results contained in `simdata`
+
+### `gel`
+
+- `data`: directory containing experimental data for the metal-crosslinked polymer hydrogel. Includes the raw data output by TRIOS (`raw`) and pre-processed CSV files for LAOS and SAOS tests
+- `fitlr.py`: Python script to fit the linear response of the gel to a single-mode Maxwell model
+- `rude.jl`: Julia script to train a RUDE using the LAOS data, and predict the shear and normal stress response in another LAOS experiment (as well as an amplitude-sweep in LAOS)
+- `weights_201.bson`: partially pre-trained model, terminated after an epoch of 200 training iterations on the lowest-amplitude LAOS experiment
+- `weights_402.bson`: partially pre-trained model, terminated after an epoch of 200 training iterations on the two lowest-amplitude LAOS experiments, with training initialized using the `weights_201.bson` network
+- `weights_603.bson`: fully pre-trained model, terminated after an epoch of 200 training iterations on all three training LAOS curves, with training initialized using the `weights_402.bson` network
+
 ## Contibuting
 
 Inquiries and suggestions can be directed to krlennon[at]mit.edu.