2024-06-13-talk-CSBQ/software.tex

% vim: set foldmethod=marker foldmarker=<<<,>>>:

\section{Software} %<<<

\begin{frame}[t,fragile] \frametitle{{CSBQ library}} \framesubtitle{{}} %<<<

  \vspace{0.5em}
  {\bf Code:} ~~ {\color{blue} \url{https://github.com/dmalhotra/CSBQ}}

  (remember to checkout submodule SCTL)

  %\vspace{0.5em}
  %{\bf Documentation:} ~~ {\color{blue} \url{https://csbq.readthedocs.io/}}

  \vspace{1.5em}
  {\bf Requirements:} ~~ {\color{red}C++11} ~compiler ~with ~{\color{red}OpenMP}

  \vspace{1.5em}
  {\bf Build system:} ~~ none (header only)

  \vspace{0.5em}
  {\bf
  \begin{minted}[
      %frame=lines,
      fontsize=\small,
      %linenos,
      gobble=0,
      mathescape
    ]{C++}
          #include <csbq.hpp>
  \end{minted}
  }



  \only<2->{
  \vspace{4em}
  {\bf Optional dependencies:} ~~ BLAS, ~~LAPACK, ~~FFTW, ~~MPI, ~~and ~~PVFMM}

  %\begin{itemize}
  %\item includes simple `Makefile' for example codes.
  %\end{itemize}

\end{frame}
%>>>

\begin{FIframe}{Library overview}{} %<<<

  \resizebox{0.91\linewidth}{!}{\begin{tikzpicture}

    \node[anchor=north west, draw=none, rounded corners=.45cm, minimum height=8.3cm, minimum width=13.5cm] at (0.65,2) {};

    \only<4->{
      \node[anchor=north west, draw=DarkGreen,thick, rounded corners=.45cm, scale=1.7] at (4.7,1.9) {\begin{tabular}{c} \bf Applications  \end{tabular}};

      \draw [line width=1mm] (0.8,0.20) -- (14.0,0.20);
    }

    \only<3->{
      \draw [->,line width=0.6mm] (2.7,-1.79) -- (2.7,-3.2);
    }

    \only<2->{
      \node[anchor=north west, draw=black,thick, rounded corners=.55cm] at (1,-0.2) {
      \begin{tabular}{c}
        {\bf CSBQ:} Convergent Slender Body Quadrature\\
        \hspace{12cm} \vspace{0.5cm}
      \end{tabular}};

      \node[anchor=north west, draw=blue,thick, rounded corners=.45cm] at  (1.25,-1.0) {\begin{tabular}{c} \bf SlenderElemL         \end{tabular}};
      \node[anchor=north west, draw=blue,thick, rounded corners=.45cm] at  (4.50,-1.0) {\begin{tabular}{c} \bf RigidBodyL, Mobility \end{tabular}};
      \node[anchor=north west, draw=blue,thick, rounded corners=.45cm] at  (9.00,-1.0) {\begin{tabular}{c} \bf CubeVolumeVis, Utils \end{tabular}};
      %\node[anchor=north west, draw=blue,thick, rounded corners=.45cm] at (12.20,-1.0) {\begin{tabular}{c} \bf Utils                \end{tabular}};
    }

    \node[anchor=north west, draw=black,thick, rounded corners=.55cm] at (1,-2.4) {
    \begin{tabular}{c}
      {\bf SCTL:} Scientific Computing Template Library\\
      \hspace{12cm} \vspace{2.39cm}
    \end{tabular}};

    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (1.50,-3.2) {\begin{tabular}{c} \bf BoundaryIntegralOp \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (6.15,-3.2) {\begin{tabular}{c} \bf Kernel             \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (8.60,-3.2) {\begin{tabular}{c} \bf FMM                \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at (10.50,-3.2) {\begin{tabular}{c} \bf Quadrature         \end{tabular}};

    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (1.50,-4.2) {\begin{tabular}{c} \bf GMRES        \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (3.95,-4.2) {\begin{tabular}{c} \bf SDC          \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (5.90,-4.2) {\begin{tabular}{c} \bf Profile      \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (8.15,-4.2) {\begin{tabular}{c} \bf Vec (SIMD)   \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at (11.30,-4.2) {\begin{tabular}{c} \bf Comm         \end{tabular}};

    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (1.50,-5.2) {\begin{tabular}{c} \bf Vector        \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (3.70,-5.2) {\begin{tabular}{c} \bf Matrix        \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (5.90,-5.2) {\begin{tabular}{c} \bf VTUData       \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at  (8.40,-5.2) {\begin{tabular}{c} \bf Interpolation \end{tabular}};
    \node[anchor=north west, draw=red,thick, rounded corners=.45cm] at (11.70,-5.2) {\begin{tabular}{c} \bf Tree          \end{tabular}};

  \end{tikzpicture}}

\end{FIframe}%>>>


\begin{FIframe}{Solving BIEs with CSBQ}{} %<<<

  \vspace{-1em}
  {\bf Step 1: Stokes Dirichlet boundary value problem (exterior)}

  \vspace{-0.5em}
  \begin{columns}[t]
    \column{0.5\textwidth}

    \begin{itemize}
      \item Stokes equations:
        \vspace{-0.5em}
        \begin{align*}
          \Delta \mathbf{u} - \nabla p &= 0 \qquad ~\mbox{ in } \mathbb{R}^3 \setminus \overline{\Omega}, \\
               \nabla \cdot \mathbf{u} &= 0 \qquad ~\mbox{ in } \mathbb{R}^3 \setminus \overline{\Omega}, \\
        \end{align*}

        \vspace{-2.5em}
      \item Boundary conditions:
        \vspace{-0.8em}
        \begin{align*}
          \mathbf{u}|_{\Gamma} &= \mathbf{u}_0 \qquad \mbox{ on } \Gamma, \\
          \mathbf{u}(\mathbf{x}) &\rightarrow \mathbf{0} \qquad \mbox{ as } |\mathbf{x}| \rightarrow \infty \\
        \end{align*}

    \end{itemize}

    \column{0.5\textwidth}

      \centering
      \vspace{2em}
      \resizebox{0.75\linewidth}{!}{\begin{tikzpicture}
        % Draw the irregular domain Omega
        \draw[fill=blue!20] plot [smooth cycle] coordinates {(1,0) (1.5,1) (2,1.5) (3,1) (3.5,0.5) (2.5,0)};
        \node at (2,1) {\(\Omega\)};
        % Draw the boundary Gamma
        \draw[line width=1.5pt] plot [smooth cycle] coordinates {(1,0) (1.5,1) (2,1.5) (3,1) (3.5,0.5) (2.5,0)};
        \node at (2.0,-0.3) {\(\Gamma = \partial\Omega \)};

        \node at (4.5,1.8) {\( \mathbb{R}^3 \setminus \overline{\Omega} \)};
      \end{tikzpicture}}

  \end{columns}

\end{FIframe}%>>>

\begin{FIframe}{Solving BIEs with CSBQ}{} %<<<

  \vspace{-1em}
  {\bf Step 2: Integral Equation Formulation}

  \vspace{-0.5em}
  \begin{columns}[t]
    \column{0.5\textwidth}

    \begin{itemize}
      \item Boundary integral representation:
        \vspace{-0.5em}
        \begin{align*}
          \mathbf{u} = \mathcal{D}[\mathbf{\sigma}] + \eta \, \mathcal{S}[\mathbf{\sigma}] \quad \mbox{ in } \mathbb{R}^3 \setminus \overline{\Omega},
        \end{align*}

        \vspace{-0.8em}
      \item[] where\\
        {\small
          \qquad $\displaystyle\mathcal{S}[\mathbf{\sigma}](\mathbf{x}) \coloneq \int_{\Gamma} S(\mathbf{x} - \mathbf{y}) \, \mathbf{\sigma}(\mathbf{y}) \, dS_{\mathbf{y}}$,

          \qquad $\displaystyle\mathcal{D}[\mathbf{\sigma}](\mathbf{x}) \coloneq \int_{\Gamma} D(\mathbf{x} - \mathbf{y}) \, \mathbf{\sigma}(\mathbf{y}) \, dS_{\mathbf{y}}$,

          \qquad $\displaystyle\eta = 1/(\epsilon \log \epsilon^{-1})$
        }

        \vspace{0.9em}
      \item Enforce boundary conditions:
        \vspace{-0.5em}
        \begin{align*}
          (I/2 + D + \eta \, S) \mathbf{\sigma} = \mathbf{u}_0 \quad \mbox{ on } \Gamma,
        \end{align*}

        \vspace{-1.0em}
      \item[] Solve for unknown { \color{red} $\sigma$ }

    \end{itemize}

    \column{0.5\textwidth}

      \centering
      \vspace{2em}
      \resizebox{0.75\linewidth}{!}{\begin{tikzpicture}
        % Draw the irregular domain Omega
        \draw[fill=blue!20] plot [smooth cycle] coordinates {(1,0) (1.5,1) (2,1.5) (3,1) (3.5,0.5) (2.5,0)};
        \node at (2,1) {\(\Omega\)};
        % Draw the boundary Gamma
        \draw[line width=1.5pt] plot [smooth cycle] coordinates {(1,0) (1.5,1) (2,1.5) (3,1) (3.5,0.5) (2.5,0)};
        \node at (2.0,-0.3) {\(\Gamma = \partial\Omega \)};

        \node at (4.5,1.8) {\( \mathbb{R}^3 \setminus \overline{\Omega} \)};
      \end{tikzpicture}}

  \end{columns}

\end{FIframe}%>>>


\begin{frame}[t,fragile] \frametitle{{Solving BIEs with CSBQ}} \framesubtitle{{}} %<<<

  \vspace{-1em}
  {\bf Step 3: Discretize the geometry}

  \vspace{-0.5em}
  \begin{columns}[t]
    \column{0.7\textwidth}

    \only<2->{
    \begin{itemize}
      \item Geometry described by centerline {\color{red} $\gamma$}.

      \only<3->{\item Partition into panels.\\
        \begin{itemize}
          \item Choose panel order and Fourier order.
        \end{itemize}
      }

      \only<4->{\item Determine nodes {\color{blue} $\mathbf{x}_c$} and radius {\color{blue} $\epsilon$}.}
    \end{itemize}
    }

    \vspace{1em}
    \only<5>{~~ Code:}
    \begin{overprint}
    \onslide<5>%<<<
    \bf
    \begin{minted}[
        %frame=lines,
        fontsize=\footnotesize,
        %linenos,
        gobble=5,
      ]{C++}
        Vector<Long> ElemOrder, FourierOrder;
        Vector<double> Xc, eps;
        // set vector data ...

        SlenderElemList<double> elem_lst(ElemOrder,
                                    FourierOrder, Xc, eps);
    \end{minted}
    %>>>
    \end{overprint}

    \column{0.4\textwidth}

    \only<1>{\includegraphics[width=0.99\textwidth]{figs/geom1}}
    \only<2>{\resizebox{0.99\linewidth}{!}{\begin{tikzpicture}
      \node[inner sep=0pt] at (0,0) {\includegraphics[width=5cm]{figs/geom2}};
      \node at (1,0) {\color{red} \( \gamma \)};
    \end{tikzpicture}}}
    \only<3>{\resizebox{0.99\linewidth}{!}{\begin{tikzpicture}
      \node[inner sep=0pt] at (0,0) {\includegraphics[width=5cm]{figs/geom3_}};
      \node at (1.3,0) {\color{red} \( \gamma_k \)};
    \end{tikzpicture}}}
    \only<4->{\resizebox{0.99\linewidth}{!}{\begin{tikzpicture}
      \node[inner sep=0pt] at (0,0) {\includegraphics[width=5cm]{figs/geom4}};
      \node at (1.3,0) {\color{red} \( \gamma_k \)};
      \node at (1.4,1.2) {\color{blue} \( \mathbf{x}_c, \epsilon \)};
    \end{tikzpicture}}}

  \end{columns}


\end{frame}
%>>>

\begin{frame}[t,fragile] \frametitle{{Solving BIEs with CSBQ}} \framesubtitle{{}} %<<<

  \vspace{-1em}
  {\bf Step 4: Discretize Integral Operator}

  \begin{itemize}
    \item {Stokes combined field kernel:}
  \end{itemize}

  {\bf
  \begin{minted}[
      %frame=lines,
      fontsize=\scriptsize,
      %linenos,
      gobble=3,
    ]{C++}
        struct Stokes3D_CF_ {
            template <Integer digits, class VecType>
            static void uKerMatrix(VecType (&u)[3][3], const VecType (&r)[3],
                                   const VecType (&n)[3], const void* ctx_ptr) {
                // u[i][j] = [Stokes-SL] + [Stokes-DL];
            }
            // other member functions ...
        };
  \end{minted}
  }
        %using Stokes3D_CF = GenericKernel<Stokes3D_CF_>;

  \vspace{-1.7em}
  \begin{overprint}
  \onslide<2>
  \begin{columns}
    \column{0.78\textwidth}
      \vspace{1em}
      \begin{itemize}
        \item {Boundary integral operator:}
      \end{itemize}

      {\bf
      \begin{minted}[
          %frame=lines,
          fontsize=\scriptsize,
          %linenos,
          gobble=3,
        ]{C++}
        Stokes3D_CF ker;
        BoundaryIntegralOp<double,Stokes3D_CF> LayerPotenOp(ker);
        LayerPotenOp.AddElemList(elem_lst); // add geometry to operator
        LayerPotenOp.SetAccuracy(tol);      // set accuracy
        
        const auto BIO = [&LayerPotenOp](Vector<double>* U,
                                         const Vector<double>& sigma) {
            LayerPotenOp.ComputePotential(*U, sigma);
            (*U) += sigma * 0.5;
        };
      \end{minted}
      }
    \column{0.23\textwidth}

    \small
    \vspace{2em}
    $\displaystyle {\mathbf u}({\mathbf x}) = (\mathcal{D} + \mathcal{S})[\sigma]({\mathbf{x}})$

    %\quad\qquad for ~~ ${\mathbf x} \in \mathbb{R}^3 \setminus \overline \Omega$

    \[ K \, \sigma \coloneq (I/2 + D + S) \, \sigma \]
  \end{columns}
  \end{overprint}

\end{frame}
%>>>


\begin{frame}[t,fragile] \frametitle{{Solving BIEs with CSBQ}} \framesubtitle{{}} %<<<

  \vspace{-1em}
  {\bf Step 5: Solve Integral Equation}
  
  \vspace{1em}
  {\bf
  \begin{minted}[
      %frame=lines,
      fontsize=\footnotesize,
      %linenos,
      gobble=4,
    ]{C++}
      Vector<double> sigma, U0(LayerPotenOp.Dim(0));
      // set boundary condition U0

      GMRES<double> solver;
      solver(&sigma, BIO, U0, tol);
  \end{minted}
  }

\end{frame}
%>>>


\begin{frame}[t,fragile] \frametitle{{Solving BIEs with CSBQ}} \framesubtitle{{}} %<<<

  \vspace{-1em}
  {\bf Step 6: Post-process}

  \vspace{1em}
  {\bf
  \begin{minted}[
      %frame=lines,
      fontsize=\footnotesize,
      %linenos,
      gobble=4,
    ]{C++}
      Vector<double> U;
      LayerPotenOp.SetTargetCoord(Xtrg); // Set targets for LayerPotenOp
      LayerPotenOp.ComputePotential(U, sigma); // Evaluate solution
      //... Write to VTK file
  \end{minted}
  }

      %CubeVolumeVis<double> cube(50, 2.0); // 50x50x50 grid, side length 2
      %LayerPotenOp.SetTargetCoord(cube.GetCoord()); // Set targets for LayerPotenOp

      %Vector<double> U;
      %LayerPotenOp.ComputePotential(U, sigma); // Evaluate solution
      %cube.WriteVTK("vis/bie-solution", U); // Write to VTK file

  \vspace{1em}
  \only<2->{
  \centering
  \includegraphics[width=0.75\textwidth]{figs/stokes-dirichlet}
  }

\end{frame}
%>>>


%>>>