Adding Documentation

doc/Sections/benchmarks.tex

@@ -3,6 +3,72 @@
 
 
 \subsection{\texttt{benchmarks-sol-ass}}
+
+This benchmark is intended to measure the computing times of the assembly of the Residue vector ($\times2$) and the
+Jacobian matrix and the solver (CGPD).
+
+Basically the benchmark executes a tipical Newton-Raphson iteration:
+
+\begin{lstlisting}
+	double norm = assembly_rhs_acc(u, nullptr, b);
+
+#ifdef _OPENACC
+	assembly_mat_acc(&A, u, nullptr);
+#else
+	assembly_mat(&A, u, nullptr);
+#endif
+
+#ifdef _OPENACC
+	int cg_its = ell_solve_cgpd_acc(&A, b, du, &cg_err);
+#else
+	int cg_its = ell_solve_cgpd(&A, b, du, &cg_err);
+#endif
+
+	for (int i = 0; i < nn * dim; ++i)
+		u[i] += du[i];
+
+	norm = assembly_rhs_acc(u, nullptr, b);
+\end{lstlisting}
+
+\begin{figure}[!htbp]
+	\centering
+	\begin{tikzpicture}[]
+		\pgfplotsset{every tick label/.append style={font=\small}}
+		\pgfplotstableread{data/benchmark-sol-ass-macintosh.dat}{\times}
+		\begin{axis}[
+%			grid=major,
+%			y unit=s,
+%			legend pos=north west,
+%			legend cell align={left},
+%			ylabel=Computing Time,
+%			xlabel=Micro-resolution,
+%			x unit=\# Elements,
+%			ymin = 0,
+%			ymax = 600,
+%			xtick = {0,20,40,60,80,100},
+%			xticklabels = {0,20\tst,40\tst,60\tst,80\tst,100\tst},
+%			ytick = {0,200,400,600,800},
+			]
+			\addplot [color=blue,mark=*,line width = 0.5mm] table [x index={0}, y index={1}] {\times};
+			\addplot [color=green,mark=*,line width = 0.5mm] table [x index={0}, y index={2}] {\times};
+%				%{\times} [yshift=9pt] 
+%				%node[pos=0.0,yshift=10pt] {36\%}
+%				%node[pos=0.105,yshift=11pt] {68\%}
+%				%node[pos=1.0] {79\%};
+%			%\addplot [color=blue ,mark=*,line width = 0.5mm]  table [x={n1}, y expr=\thisrowno{2}*1.0e-6]
+%				%{\times} [yshift=9pt] 
+%				%node[pos=0.0] {64\%}
+%				%node[pos=0.253,yshift=5pt] {32\%}
+%				%node[pos=1.0] {21\%};
+%			%\legend{Jacobian \& Residue Assembly}
+		\end{axis}
+	\end{tikzpicture}
+%	\caption{\label{fig:ass_vs_sol}
+%		Computing time used for the assembly of the Jacobian Matrix and the Residue vector and the solver
+%		algorithm of the Micropp code to perform the micro-scale FE calculation.
+%	}
+\end{figure}
+
 \subsection{\texttt{benchmarks-cpu-gpu}}
 \subsection{\texttt{benchmarks-elastic}}
 \subsection{\texttt{benchmarks-plastic}}

doc/Sections/compilation.tex

+\section{Coding Style}
+
+The compilation process is based on \texttt{CMake}
+

doc/data/benchmark-sol-ass-macintosh.dat

+#N    time_ass   time_sol    ass%     sol%
+10	16	14	17.0333	46.6667
+20	111	174	9.42105	61.0526
+30	374	818	7.62248	68.6242
+40	887	2539	6.06713	74.1097
+50	1746	5858	5.52854	77.0384
+60	3026	11838	4.91247	79.6421
+70	4920	21121	4.62932	81.1067
+80	7381	35436	4.42215	82.7615
+90	10379	56179	4.03812	84.4061
+100	14259	83713	3.69338	85.4458

doc/manual.tex

 \documentclass[conference, onecolumn]{IEEEtran}
-% \usepackage[pdftex]{graphicx}
-% \usepackage[dvips]{graphicx}
-%\usepackage{amsmath}
+
 \usepackage{algorithm}
 \usepackage{algorithmic}
-%\usepackage{array}
-%\usepackage[caption=false,font=normalsize,labelfont=sf,textfont=sf]{subfig}
-%\usepackage{fixltx2e}
-%\usepackage{stfloats}
-%\usepackage{url}
 \usepackage{amsmath}
 \usepackage{amssymb}
 \RequirePackage{amsfonts}
-\RequirePackage{standalone}
-\RequirePackage{tikz}
-\usetikzlibrary{matrix,backgrounds,calc,shapes,arrows,arrows.meta,fit,positioning}                                                                
-\usetikzlibrary{chains,shapes.multipart}                                                                                                          
-\usetikzlibrary{shapes,calc} 
-
+\usepackage{siunitx}
+\usepackage{standalone}
+\usepackage{tikz}
+\usetikzlibrary{matrix,backgrounds,calc,shapes,arrows,arrows.meta,fit,positioning}
+\usetikzlibrary{chains,shapes.multipart}
+\usepackage{pgfplots, pgfplotstable}
+\usepgfplotslibrary{units}
+\usepackage{xcolor}
+\usepackage{xspace}
 \usepackage{listings}
 \usepackage{color}
 
@@ -196,7 +192,8 @@ f_{n+1}^{\text{trial}} = || s_{n+1}^{\text{trial}} || - \sqrt{\frac{2}{3}} (\sig
 \end{algorithmic}
 \end{algorithm}
 
-\input{coding_style.tex}
+\input{Sections/compilation.tex}
+\input{Sections/coding_style.tex}
 
 \input{Sections/benchmarks.tex}
 
@@ -206,12 +203,28 @@ The conclusion goes here.
 % use section* for acknowledgment
 \section*{Acknowledgment}
 
-The authors would like to thank to the Barcelona Supercomputing Center for the resources provided to develop and test \emph{micropp} code in the architectures: \emph{Marenostrum IV} \& \emph{CTE-POWER} during Sep., 2016 and Dic., 2019. The simulations were primary done coupling \emph{micropp} with the multi-physics code \emph{Alya} to solve the macro-scale equations.
+The authors would like to thank to the Barcelona Supercomputing Center for the resources provided to develop and test Micropp code in the architectures: Marenostrum IV \& CTE-POWER during Sep., 2016 and Dic., 2019. The simulations were primary done coupling Micropp with the multi-physics code Alya to solve the macro-scale equations.
 
 \begin{thebibliography}{1}
-\bibitem{paper1}G. Giuntoli, J. Aguilar, M. Vazquez, S. Oller and G. Houzeaux. \textit{A FE$^2$ multi-scale implementation for modeling composite materials on distributed architectures}. Coupled Systems Mechanics, 8(2), 2018
-\bibitem{simo} J.C. Simo \& T.J.R. Huges.\emph{Computational Ineslasticity}, Springer, 2000. 
-\bibitem{oller} S. Oller. \emph{Numerical Simulation of Mechanical Behavior of Composite Materials}, Springer, 2014. 
+
+	\bibitem{paper1}{
+		G. Giuntoli, J. Aguilar, M. Vazquez, S. Oller and G. Houzeaux.
+		``An FE$^2$ multi-scale	implementation for modeling composite materials on distributed architectures''. 
+		Coupled Systems Mechanics, 8(2), 2018
+	}
+
+	\bibitem{simo}{
+		J.C. Simo \& T.J.R. Huges.
+		``Computational Ineslasticity''.
+		Springer, 2000. 
+	}
+
+	\bibitem{oller}{
+		S. Oller.
+		``Numerical Simulation of Mechanical Behavior of Composite Materials''.
+		Springer, 2014. 
+	}
+
 \end{thebibliography}
 
 \end{document}

test/benchmark-sol-ass.cpp

@@ -115,10 +115,10 @@ class test_t : public micropp<3> {
 				<< "sol : " << percentage_sol << " \%" << endl;
 			cout << "|r| : " << norm << endl;
 			file
-				<< nx - 1 << " "
-				<< ass_res.count() + ass_mat.count() << " "
-				<< solver.count() << " "
-				<< percentage_ass << " "
+				<< nx - 1 << "\t"
+				<< ass_res.count() + ass_mat.count() << "\t"
+				<< solver.count() << "\t"
+				<< percentage_ass << "\t"
 				<< percentage_sol << endl;
 
 			ell_free(&A);