manuscript.tex

%&pdflatex
\documentclass[pdftex,preprint,3p,times,numbers]{elsarticle}

\journal{Computer Physics Communications}

%\usepackage{moreverb}

\usepackage{hyperref}
\hypersetup{pdfborder={0 0 0}}

\usepackage{float}
\usepackage{wrapfig}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{multirow}
\graphicspath{{images/}}

\usepackage[pdftex,usenames]{xcolor}

\usepackage{booktabs}
%\usepackage{colortbl}
\usepackage{multirow}

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage[utf8x]{inputenc}
\usepackage[T1]{fontenc}

\usepackage{xspace}

\usepackage{xcolor}
\definecolor{Maroon}{cmyk}{0,0.87,0.68,0.32}
\definecolor{RoyalBlue}{cmyk}{1,0.50,0,0}
\definecolor{gray}{cmyk}{0.01,0.01,0.01,0.01}
\usepackage{listings}
\lstdefinelanguage{MyFortran}[08]{Fortran}{morecomment=[l]{\#},morestring=[d]',morekeywords={procedure,pass,deferred,non_overridable,generic,class,is}}
\lstdefinestyle{code}{%
  basicstyle=\footnotesize,%
  backgroundcolor=\color{gray},%
  language=MyFortran,%
  captionpos=b,%
  columns=fixed,%
  keepspaces=true,%
  xleftmargin=10pt,%
  numbers=none,%
  numberstyle={\tiny},%
  keywordstyle=\color{RoyalBlue},%
  % stringstyle={\sffamily},%
  texcl=true,%
  upquote=true,%
  commentstyle=\color{Maroon}%
}

\lstdefinestyle{codesimple}{%
  basicstyle=\footnotesize,%
  backgroundcolor=\color{gray},%
  captionpos=b,%
  columns=fixed,%
  keepspaces=true,%
  xleftmargin=10pt,%
  numbers=none,%
}

\DeclareSymbolFont{extraup}{U}{zavm}{m}{n}
\DeclareMathSymbol{\vardiamond}{\mathalpha}{extraup}{87}
\definecolor{OMP}{RGB}{255,127,0}
\definecolor{MPI}{RGB}{0,127,255}
\definecolor{HYB}{RGB}{127,0,255}

\DeclareGraphicsExtensions{.pdf,.png,.jpg,.bmp,.mps}
\newcommand{\citeh}[1]{\citeauthor{#1} \citenum{#1}}

\renewcommand{\thesubfigure}{\Alph{subfigure}}

\begin{document}

\begin{frontmatter}

\title{FOODIE, Fortran Object oriented Ordinary Differential Equations integration library based on Abstract Calculus Pattern}

\author[insean]{Zaghi S.\corref{cor1}\fnref{sz}}
\ead{stefano.zaghi@cnr.it}
\fntext[sz]{Ph. D., Aerospace Engineer, Research Scientist, Dept. of Computational Hydrodynamics at CNR-INSEAN.}
\address[insean]{CNR-INSEAN, Istituto Nazionale per Studi ed Esperienze di Architettura Navale, Via di Vallerano 139, Rome, Italy, 00128}
\cortext[cor1]{Corresponding author}

\author[rsmas]{Curcic M.\fnref{mc}}
\ead{milan@orca.rsmas.miami.edu}
\fntext[mc]{Ph.D. Meteorology and Physical Oceanography, Research Scientist, Dept. of Ocean Sciences Rosenstiel School of Marine and Atmospheric Science at University of Miami}
\address[rsmas]{Ocean Sciences Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway Miami, FL 33149-1098 +1 305.421.4000}

\author[sourcery]{Rouson D.\fnref{dr}}
\ead{damian@sourceryinstitute.org}
\fntext[dr]{Ph.D. Mechanical Engineering, Founder and President Sourcery Institute and Sourcery, Inc.}
\address[sourcery]{Sourcery Institute 482 Michigan Ave., Berkeley, CA 94707}

\author[sourcery]{Beekman I.\fnref{iz}}
\ead{izaak@izaakbeekman.com}
\fntext[iz]{Graduate Research Assistant, Princeton/UMD CCROCCO LAB}

\begin{abstract}
The (numerical) solution of Ordinary Differential Equations (ODEs) problems is of paramount relevance, ODEs system being an ubiquitous mathematical formulation of many physical phenomena (such as those involved in fluid dynamics, chemistry, biology, evolutionary-anthropology, \dots). The present paper is the first \emph{manifesto} of FOODIE, a library aimed to numerically solve ODEs problems by means of a clear, concise and efficient \emph{abstract} interface. FOODIE, meaning Fortran Object oriented Ordinary Differential Equations integration library, has manifolds aims: to provide a set to built-in numerical schemes that are accurate, robust, validated and efficient and to allow easy application of these schemes to (almost) all ODEs problems by means of an effective Abstract Calculus Pattern. The key idea is to allow the same solver-implementation to be applied to all ODEs problems thus avoiding the re-implementation of the ODEs solver for each different ODEs problem: code re-usability is consequently maximized, FOODIE being a general robust framework. Besides, the same framework also allows rapid development of new ODEs solvers due to the high abstraction level of the library itself.

FOODIE is a modern Fortran library which main features are:
\begin{description}
  \item[Free] FOODIE is a free software;
  \item[OOP] FOODIE is based on Object Oriented Programming paradigm;
  \item[TDD] the FOODIE development follows the Test Driven Development software process;
  \item[Accurately documented] the FOODIE documentation is based on high quality, first class solutions embedding detailed (mathematical) descriptions directly inside code sources; moreover, comprehensive hyper-linked documentations is also provided;
  \item[Comphrensive] FOODIE provides a comprehensive set of built-in solvers, namely one-step, multi-steps, explicit, implicit, predictor-corrector solvers; moreover, its Abstract Calculus Pattern allows the solution of virtually all kinds of ODEs problems;
  \item[Collaborative] the development of FOODIE takes advantage of web communications, the main project being hosted on GitHub.
\end{description}

The present paper is the first announcement of FOODIE project: the current implementation is extensively discussed and its capabilities are proved by means of tests and examples.
\end{abstract}

\begin{keyword}
  Ordinary Differential Equations (ODE) \sep
  Partial Differential Equations (PDE) \sep
  Object Oriented Programming (OOP) \sep
  Abstract Calculus Pattern (ACP) \sep
  Fortran
\end{keyword}

\end{frontmatter}

{\bf PROGRAM SUMMARY}

\begin{small}
\noindent
\emph{Manuscript Title:} FOODIE, Fortran Object oriented Ordinary Differential Equations integration library based on Abstract Calculus Pattern \\
\emph{Authors:} Zaghi, S., Curcic, M., Rouson, D., Beekman, I. \\
\emph{Program title:} FOODIE \\
\emph{Journal Reference:} \\
\emph{Catalogue identifier:} \\
\emph{Licensing provisions:} GNU General Public License (GPL) v3 \\
\emph{Programming language:} Fortran (standard 2008 or newer); developed and tested with GNU gfortran 5.2 or newer \\
\emph{Computer(s) for which the program has been designed:} designed for shared-memory multi-cores workstations and for hybrid distributed/shared-memory supercomputers, but any computer system with a Fortran (2008+) compiler is suited \\
\emph{Operating system(s) for which the program has been designed:} designed for POSIX architecture and tested on GNU/Linux one \\
\emph{RAM required to execute with typical data: bytes:} $[1MB,1GB]\times core$, simulation-dependent \\
\emph{Has the code been vectorised or parallelized?:} the library is not aware of the parallel back-end, it providing a high-level models, but the provided tests suite shows parallel usage by means of MPI library and OpenMP paradigm \\
\emph{Number of processors used:} tested up to 256 \\
\emph{Supplementary material:}    \\
\emph{Keywords:} ODE, PDE, OOP, ACP, Fortran \\
\emph{CPC Library Classification:} 4.3 Differential Equations, 4.10 Interpolation, 12 Gases and Fluids \\
\emph{External routines/libraries used:} \\
\emph{CPC Program Library subprograms used:} \\
\emph{Nature of problem:} \\
Numerical integration of (general) Ordinary Differential Equations system \\
\emph{Solution method:} \\
\emph{Restrictions:} \\
\emph{Unusual features:} \\
\emph{Additional comments:} \\
\emph{Running time:} \\
\emph{References:} \\
% \begin{thebibliography}{0}
% \end{thebibliography}
\end{small}

\input{src/introduction/introduction.tex}

\clearpage

\input{src/mathematical-numerical-models/mathematical-numerical-models.tex}

\clearpage

\input{src/API/API.tex}

\clearpage

\input{src/tests/tests.tex}

\clearpage

\input{src/parallel/parallel.tex}

\clearpage

\input{src/conclusions/conclusions.tex}

\appendix

\input{src/appendix/euler-1D-parallel-tests-API.tex}

\bibliographystyle{mycpc2}
\bibliography{Reference}

\end{document}