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naaice/README.md

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+
+This directory contains a concise benchmark designed for validating FPGA
+offloading of the Thomas algorithm, primarily employed for solving linear
+equation systems structured within a tridiagonal matrix.
+
+
+# Benchmark Setup
+
+The benchmark involves a domain measuring $0.5 \text{cm} \times 1 \text{cm}$,
+divided into a grid of dimensions $10 \times 5$. Each grid cell initially
+contains a specific concentration. The concentration in the first half along the
+x-dimension is set at $6.92023 \times 10^{-7}$, while in the second half, it’s
+$2.02396 \times 10^{-8}$, creating a concentration gradient along the y-axis at
+the center of the grid.
+
+To achieve concentration equilibrium, we employ a simulation based on a
+heterogeneous 2D-ADI BTCS diffusion approach, detailed in the
+[ADI<sub>scheme.pdf</sub>](../doc/ADI_scheme.pdf) file. In the x-direction,
+diffusion coefficients range from $\alpha = 10^{-9}$ to $10^{-10}$, while in the
+y-direction, a constant value of $5 \times 10^{-10}$ is applied. A closed
+boundary condition is implemented, meaning concentrations cannot enter or exit
+the system. The diffusion process is simulated for a single iteration with a
+time step ($\Delta t$) of 360 seconds.
+
+
+# Setup
+
+To generate new makefiles using the `-DTUG_NAAICE_EXAMPLE=ON` option in CMake,
+compile the executable, and run it to generate the benchmark output, follow
+these steps:
+
+1.  Navigate to your project's build directory.
+2.  Run the following CMake command with the `-DTUG_NAAICE_EXAMPLE=ON` option to
+    generate the makefiles:
+    
+        cmake -DTUG_NAAICE_EXAMPLE=ON ..
+
+3.  After CMake configuration is complete, build the `naaice` executable by running `make`:
+    
+        make naaice
+
+4.  Once the compilation is successful, navigate to the build directory by `cd
+       <build_dir>/naaice`
+
+5.  Finally, run the `naaice` executable to generate the benchmark output:
+    
+        ./naaice
+
+
+## Output Files
+
+
+### `Thomas_<n>.csv`
+
+These files contain the values of the tridiagonal coefficient matrix $A$, where:
+
+-   $Aa$ represents the leftmost value,
+-   $Ab$ represents the middle value, and
+-   $Ac$ represents the rightmost value of one row of the matrix.
+
+Additionally, the corresponding values of the right-hand-side vector $b$ are
+provided.
+
+Since the 2D-ADI BTCS scheme processes each row first and then proceeds
+column-wise through the grid, each iteration is saved separately in
+consecutively numbered files.
+
+
+### `BTCS_5_10_1.csv`
+
+The result of the simulation, **separated by whitespaces**!
+

naaice/README.org

@@ -1,72 +0,0 @@
-#+title: NAAICE Benchmark
-
-This directory contains a concise benchmark designed for validating FPGA
-offloading of the Thomas algorithm, primarily employed for solving linear
-equation systems structured within a tridiagonal matrix.
-
-* Benchmark Setup
-
-The benchmark involves a domain measuring $0.5 \text{cm} \times 1 \text{cm}$,
-divided into a grid of dimensions $10 \times 5$. Each grid cell initially
-contains a specific concentration. The concentration in the first half along the
-x-dimension is set at $6.92023 \times 10^{-7}$, while in the second half, it's
-$2.02396 \times 10^{-8}$, creating a concentration gradient along the y-axis at
-the center of the grid.
-
-To achieve concentration equilibrium, we employ a simulation based on a
-heterogeneous 2D-ADI BTCS diffusion approach, detailed in the [[file:../doc/ADI_scheme.pdf][ADI_scheme.pdf]]
-file. In the x-direction, diffusion coefficients range from $\alpha = 10^{-9}$
-to $10^{-10}$, while in the y-direction, a constant value of $5 \times 10^{-10}$
-is applied. A closed boundary condition is implemented, meaning concentrations
-cannot enter or exit the system. The diffusion process is simulated for a single
-iteration with a time step ($\Delta t$) of 360 seconds.
-
-* Setup
-
-To generate new makefiles using the =-DTUG_NAAICE_EXAMPLE=ON= option in CMake,
-compile the executable, and run it to generate the benchmark output, follow
-these steps:
-
-1. Navigate to your project's build directory.
-2. Run the following CMake command with the =-DTUG_NAAICE_EXAMPLE=ON= option to
-   generate the makefiles:
-
-    #+BEGIN_SRC sh
-    cmake -DTUG_NAAICE_EXAMPLE=ON ..
-    #+END_SRC
-
-3. After CMake configuration is complete, build the =naaice= executable by running =make=:
-
-    #+BEGIN_SRC sh
-    make naaice
-    #+END_SRC
-
-4. Once the compilation is successful, navigate to the build directory by =cd
-   <build_dir>/naaice=
-
-5. Finally, run the =naaice= executable to generate the benchmark output:
-
-    #+BEGIN_SRC sh
-    ./naaice
-    #+END_SRC
-
-** Output Files
-
-*** =Thomas_<n>.csv=
-
-These files contain the values of the tridiagonal coefficient matrix $A$, where:
-
-- $Aa$ represents the leftmost value,
-- $Ab$ represents the middle value, and
-- $Ac$ represents the rightmost value of one row of the matrix.
-
-Additionally, the corresponding values of the right-hand-side vector $b$ are
-provided.
-
-Since the 2D-ADI BTCS scheme processes each row first and then proceeds
-column-wise through the grid, each iteration is saved separately in
-consecutively numbered files.
-
-*** =BTCS_5_10_1.csv=
-
-The result of the simulation, *separated by whitespaces*!