From: Daniel Arndt Date: Tue, 24 Apr 2018 14:36:15 +0000 (+0200) Subject: Update references to newly supported libraries X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=ab7d4de6cf3a44dca0eccaadb9c15e818e891a7c;p=release-papers.git Update references to newly supported libraries --- diff --git a/9.0/paper.bib b/9.0/paper.bib index 451bdbe..40b1fc5 100644 --- a/9.0/paper.bib +++ b/9.0/paper.bib @@ -668,3 +668,27 @@ year = {2009} year={2014}, institution={Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)} } + +@BOOK{slug, + AUTHOR = {Blackford, L. S. and Choi, J. and Cleary, A. and + D'Azevedo, E. and Demmel, J. and Dhillon, I. and + Dongarra, J. and Hammarling, S. and Henry, G. and + Petitet, A. and Stanley, K. and Walker, D. and + Whaley, R. C.}, + TITLE = {{ScaLAPACK} Users' Guide}, + PUBLISHER = {Society for Industrial and Applied Mathematics}, + YEAR = {1997}, + ADDRESS = {Philadelphia, PA}, + ISBN = {0-89871-397-8 (paperback)} +} + +@article{geuzaine2009gmsh, + title={Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities}, + author={Geuzaine, Christophe and Remacle, Jean-Fran{\c{c}}ois}, + journal={International journal for numerical methods in engineering}, + volume={79}, + number={11}, + pages={1309--1331}, + year={2009}, + publisher={Wiley Online Library} +} diff --git a/9.0/paper.tex b/9.0/paper.tex index f023adf..f3ac63b 100644 --- a/9.0/paper.tex +++ b/9.0/paper.tex @@ -185,9 +185,6 @@ following section. In addition, this release contains the following changes: and Coverity Scan \cite{coverity} static analysis tools for detecting bugs and other issues in the code. For example, around 260 issues were detected and fixed using the latter tool. - %% > Is there somewhere we can cite for either of these tools? It would - %% > be nice to recognize the department of homeland security for offering - %% The contract with homeland security was completed in 2009. \item \texttt{LinearOperator}, a flexible template class that implements the action of a @@ -200,7 +197,7 @@ following section. In addition, this release contains the following changes: \item New non-standard quadrature rules: A number of non-standard, special-purpose quadrature rules have been implemented. Among these are ones for -(i) truncating standard formulas to simplical domains (\texttt{Qsimplex}); +(i) truncating standard formulas to simplical domains (\texttt{QSimplex}); (ii) singular transformations of the unit cell to the unit simplex (\texttt{QDuffy}); (iii) composition of simplical quadrature rules to a combined rule on the @@ -360,12 +357,38 @@ re-implementing their functionality. (A list of interfaces to other packages is given in Section~\ref{sec:cite}.) As part of the current release, we have written several new interfaces as discussed in the following. -\marginpar{Add references to all of these libraries.} +\paragraph*{Assimp, the Open Asset Import Library.} + Assimp \cite{assimp} can be used to read about 40 different 3D + graphics formats. A subset of these formats can be now be read from + within \dealii to generate two-dimensional meshes, possibly embedded in + a three-dimensional space. + +% \paragraph*{Gmsh.} +% \marginpar{Do we actually provide any functionality with the GMSH +% executable yet? If so, complete this part} +% Gmsh \cite{geuzaine2009gmsh} +% The only thing we currently do is to define DEAL_II_GMSH_EXECUTABLE_PATH + +\paragraph*{nanoflann, a library for building and querying + $k$-d trees of datasets.} Operations such as finding the vertex or cell + closest to a given evaluation point occur frequently in many applications + that use unstructured meshes. While the naive algorithm is linear in the + number of vertices or cells, many such operations can be made significantly + faster by building a $k$-d tree data structure that recursively subdivides + a $k$ dimensional space. The nanoflann library \cite{nanoflann} provides + such a data structure and allows querying it, either for closest points + (e.g., when finding the closest vertex) or for searching the points that + fall within a radius of a target point. This functionality is now available + via \dealii interfaces. + +\paragraph*{ROL, a Rapid Optimization Library.} + ROL \cite{ridzal2014rapid} is a package for large-scale optimization. + \marginpar{Can we add a sentence or two about the ROL interface here?} \paragraph*{ScaLAPACK, a parallel dense linear algebra library.} - ScaLAPACK provides block-cyclic matrix distribution over 2D process - grid. The functionality and interface of our wrappers is similar to - the LAPACK wrappers for serial dense linear algebra, namely + ScaLAPACK \cite{slug} provides block-cyclic matrix distribution over 2D + process grid. The functionality and interface of our wrappers is similar + to the LAPACK wrappers for serial dense linear algebra, namely matrix-matrix multiplication, Cholesky and LU factorizations, eigensolvers, SVD, pseudoinverses, and save/load operations using the HDF5 format. All of this functionality is available even in @@ -382,8 +405,8 @@ release, we have written several new interfaces as discussed in the following. Equation Solvers.} Solving nonlinear algebraic and differential equations is both a common task and one that often requires sophisticated globalization - algorithms for efficiency and reliability. SUNDIALS provides these - in a widely used format, both sequentially and in parallel. + algorithms for efficiency and reliability. SUNDIALS \cite{sundials} + provides these in a widely used format, both sequentially and in parallel. \dealii now has interfaces to SUNDIALS's ARKode, IDA, and KINSOL sub-packages. ARKode is a solver library that provides adaptive-step time @@ -391,34 +414,6 @@ release, we have written several new interfaces as discussed in the following. equations systems in the form $F(t,y,y')=0$. KINSOL is solver for nonlinear algebraic systems. -\paragraph*{ROL, a Rapid Optimization Library.} -ROL is a package for large-scale optimization. -\marginpar{Can we add a sentence or two about the ROL interface here?} - -\paragraph*{nanoflann, a library for building and querying - $k$-d trees of datasets.} Operations such as finding the vertex -or cell closest -to a given evaluation point occur frequently in many applications that -use unstructured meshes. While the naive algorithm is linear in the -number of vertices or cells, many such operations can be made -significantly faster by building a $k$-d tree data structure that -recursively subdivides a $k$ dimensional space. The nanoflann library -provides such a data structure and allows querying it, either for -closest points (e.g., when finding the closest vertex) or for -searching the points that fall within a radius of a target point. This -functionality is now available via \dealii interfaces. - -\paragraph*{Assimp, the Open Asset Import Library.} - Assimp can be used to read about 40 different 3D graphics formats. A - subset of these formats can be now be read from within \dealii to - generate two-dimensional meshes, possibly embedded in a - three-dimensional space. - -\paragraph*{Gmsh.} - \marginpar{Do we actually provide any functionality with the GMSH - executable yet? If so, complete this part} - - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{Use of C++11} \label{sec:cxx11} @@ -639,7 +634,7 @@ following: \item ARPACK \cite{arpack} \item Assimp \cite{assimp} \item BLAS and LAPACK -\item Gmsh \cite{...} +\item Gmsh \cite{geuzaine2009gmsh} \item GSL \cite{gsl2016} \item HDF5 \cite{hdf5} \item METIS \cite{karypis1998fast} @@ -651,7 +646,7 @@ following: \item p4est \cite{p4est} \item PETSc \cite{petsc-user-ref,petsc-web-page} \item ROL \cite{ridzal2014rapid} -\item ScaLAPACK +\item ScaLAPACK \cite{slug} \item SLEPc \cite{Hernandez:2005:SSF} \item SUNDIALS \cite{sundials} \item TBB \cite{Rei07}