updated README

2 files changed, 104 insertions, 18 deletions

diff --git a/README.md b/README.md
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+++ b/README.md
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 # benchmark_suite_IREU
 A benchmark suite for memristive and memcapacitive crossbar computing systems
 
-## overview
-The memristive computing field lacks standardized benchmarks that control for workload characteristics, expose
-device-type differences, and report results comparable to conventional CMOS hardware. This project designs,
-implements, and releases a benchmark suite targeting memristive and memcapacitive crossbar architectures on
-CMOS substrates.
+## Research question
+How does a chosen device subcircuit affect the same computing system? 
+
+The memristive computing field lacks standardized benchmarks that control for 
+workload characteristics, expose device-type differences, and report results 
+comparable to conventional CMOS hardware. This project designs, implements, and 
+releases a benchmark suite targeting memristive and memcapacitive crossbar 
+architectures on CMOS substrates.
+
+## abstract
+MemDevice Benchmark is a benchmarking framework for simulated memristor crossbar's 
+using reservoir computing tasks as standardized workloads with the goal of revealing 
+unique device model effects. The framework evaluates memristor devices under the 
+same circuit, network, and workload characteristics. In the proposed architecture 
+the SPICE crossbar is implemented as the readout layer for a reservoir computer.
+Ridge regressiong training is done on a software reservoir, training the software 
+weights. An input series is given to the reservoir, the resulting temporal states 
+are  converted into voltage signals applied to the crossbar rows. The trained readout 
+weights are converted into equivalent resistances to serve as the initial device 
+values. The crossbar columns are read and mapped back to human readable data that 
+prove task prediciton capability.
+
+Because the reservoir, crossbar, training procedure and benchmark tasks remain fixed, 
+different SPICE device models can be hot swapped and benchmarked in one continous 
+process, making fair comparisons possible and observing how device model choice 
+affects the same computing system
+
+## Setup
+**Download Spires:**   
+git clone https://github.com/txmastin/spires.git   
+cd spires   
+make   
+
+**Download plplot:**   
+git clone git://git.code.sf.net/p/plplot/plplot plplot.git   
+cd plplot.git   
+mkdir build   
+cd build   
+make   
+sudo make install   
+
+**Other dependencies may be required for the listed libraries**
+
+**from the projects root directory (~/MemDevice_Benchmark/)**    
+make run   
+
+## 
diff --git a/src/README.md b/src/README.md
index cff34af..5d0dcb0 100644
--- a/src/README.md
+++ b/src/README.md
@@ -1,20 +1,64 @@
-OH MY GOD SO MUCH HAS CHANGED NEED TO UPDATE
+# public api
+## benchmark.c
 
-# memristor crossbar readout layer for reservoir computer
-##setup 
-### download spires
+The public API for running crossbar simulation, calculating performance metrics,
+and generating plots.
 
-## overview
-### simulation
+* **MemModel struct**
+    * This is a struct for making model swapping easier
+    * members
+        * const char *model_path
+        * const char *subcircuit_name
 
-### benchmark
+* **run_benchmark() (int)**
+    * Executes the full crossbar simulation pipeline and stores the decoded
+    crossbar predictions in the passed output array.
+    * parameters
+        * const spires_reservoir_config *config
+        * spires_reservoir *reservoir
+        * Reservoir_State_Matrix *state_matrix
+        * const char *model_path
+        * const char *subcircuit_name
+        * double *predictions_out
 
-## Goal
-The goal is to able to simulate a spires reservoir on a memristor crossbar using
-a custom memristor spice model(HIL), thus you can run the same simulation with 
-multiple models to compare how each performs using benchmark results.
+* **calculate_MSE() (double)**
+    * calculates the mean squared error of the predictions against the expected
+    values
+    * parameters
+        * const double *expected
+        * const double *predicted
+        * const size_t *num_steps
+        * const size_t num_outputs
 
-## task
+* **plot_raster() (int)**
+    * generates a raster plot of the reservoir based on the spike threshhold parameter
+    (not that useful tbh but can be cool to see), plot stored as svg in output directory
+    * parameters
+        * const Reservoir_State_Matrix *matrix
+        * const size_t neurons_to_plot
+        * const double spike_threshold
+
+* **plot_reservoir_predictions() (int)** 
+    * plots the decoded crossbar predictions against the expected values, plot stored
+    as svg in output directory with name "reservoir_prediction_$(model_name).svg"
+    * parameters
+        * const double *expected
+        * const double *predicted
+        * size_t num_samples
+        * size_t num_outputs
+        * size_t output_to_plot
+        * const char *model_path
+
+* **plot_model_delta() (int)**
+    * plots the prediction differences for every timestep between the given model
+    and the fixed resistor baseline
+    * parameters
+        * const double *fixed
+        * const double *model
+        * const size_t num_samples
+        * const size_t num_outputs
+        * const size_t output_to_plot
+
+# Internal header files
 
-## metrics