From 9bf48165647731dd1a9a53f3e51574f914526b5e Mon Sep 17 00:00:00 2001 From: Peter Munch Date: Sat, 18 May 2024 13:22:22 +0200 Subject: [PATCH] Consistently use cite --- doc/doxygen/references.bib | 135 ++++++++++++++++ .../deal.II/algorithms/general_data_storage.h | 14 +- .../deal.II/base/parsed_convergence_table.h | 14 +- include/deal.II/base/symmetric_tensor.h | 150 ++---------------- include/deal.II/fe/fe_bernardi_raugel.h | 16 +- include/deal.II/lac/qr.h | 42 +---- include/deal.II/lac/utilities.h | 27 +--- include/deal.II/meshworker/scratch_data.h | 14 +- .../deal.II/optimization/line_minimization.h | 23 +-- include/deal.II/physics/notation.h | 28 +--- 10 files changed, 155 insertions(+), 308 deletions(-) diff --git a/doc/doxygen/references.bib b/doc/doxygen/references.bib index 3194268c9d..d1cb7189ee 100644 --- a/doc/doxygen/references.bib +++ b/doc/doxygen/references.bib @@ -2479,3 +2479,138 @@ year = {2009}, } +@book{Fletcher2013, + title = {Practical methods of optimization}, + publisher = {John Wiley \& Sons}, + year = {2013}, + author = {Fletcher, Roger}, + isbn = {978-0-471-49463-8}, + doi = {10.1002/9781118723203}, +} + +@article{Kopp2008, + title = {Efficient numerical diagonalization of hermitian 3x3 + matrices}, + author = {Kopp, J.}, + journal = {International Journal of Modern Physics C}, + year = {2008}, + volume = {19}, + number = {3}, + pages = {523--548}, + doi = {10.1142/S0129183108012303}, + eprinttype = {arXiv}, + eprint = {physics/0610206v3}, + eprintclass = {physics.comp-ph}, + url = {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} +} + +@book{Press2007, + title = {Numerical recipes 3rd edition: The art of scientific computing}, + author = {Press, W. H.}, + journal = {Cambridge university press}, + year = {2007} +} + +@article{SartoriGiulianiBardelloni-2018-a, + Author = {Sartori, Alberto and Giuliani, Nicola and Bardelloni, Mauro and Heltai, Luca}, + Journal = {SoftwareX}, + Pages = {318--327}, + Title = {{deal2lkit: A toolkit library for high performance programming in deal.II}}, + Doi = {10.1016/j.softx.2018.09.004}, + Volume = {7}, + Year = {2018} +} + +@article{Zhou2006, + Title = {Self-consistent-field Calculations Using Chebyshev-filtered Subspace Iteration}, + Author = {Zhou, Yunkai and Saad, Yousef and Tiago, Murilo L. and + Chelikowsky, James R.}, + Journal = {Journal of Computational Physics}, + Year = {2006}, + Volume = {219}, + Pages = {172--184}, +} + +@article{Zhou2014, + Title = {Chebyshev-filtered subspace iteration method free of sparse + diagonalization for solving the Kohn--Sham equation}, + Author = {Zhou, Yunkai and Chelikowsky, James R and Saad, Yousef}, + Journal = {Journal of Computational Physics}, + Year = {2014}, + Volume = {274}, + Pages = {770--782}, + } + +@book{Golub2013, + title = {Matrix computations}, + publisher = {Johns Hopkins University Press}, + year = {2013}, + author = {Golub, Gene H and Van Loan, Charles F}, + edition = {4}, +} + +@article{Daniel1976, + author = {Daniel, James W and Gragg, Walter Bill and Kaufman, Linda and Stewart, Gilbert W}, + title = {{Reorthogonalization and stable algorithms for updating the Gram-Schmidt QR factorization}}, + journal = {Mathematics of Computation}, + year = {1976}, + volume = {30}, + number = {136}, + pages = {772--795}, +} + +@article{Reichel1990, + author = {Reichel, L. and Gragg, W. B.}, + title = {{Algorithm 686: FORTRAN Subroutines for Updating the QR Decomposition}}, + journal = {ACM Trans. Math. Softw.}, + year = {1990}, + volume = {16}, + number = {4}, + pages = {369--377}, + month = dec, + issn = {0098-3500}, + acmid = {98291}, + address = {New York, NY, USA}, + doi = {10.1145/98267.98291}, + issue_date = {Dec. 1990}, + numpages = {9}, + publisher = {ACM}, + url = {http://doi.acm.org/10.1145/98267.98291}, +} + +@article{BR85, + author = {Christine Bernardi and Genevi{\`e}ve Raugel}, + title = {Analysis of some finite elements for the {S}tokes problem}, + journal = {Mathematics of Computation}, + publisher = {American Mathematical Society ({AMS})}, + volume = {44}, + number = {169}, + pages = {71--79}, + year = {1985}, + doi = {10.1090/s0025-5718-1985-0771031-7}, + url = {https://doi.org/10.1090/s0025-5718-1985-0771031-7} + } + +@article{Nagel2016, + author = {Nagel, T. and G{\"o}rke, U-J. and Moerman, K. and Kolditz, + O.}, + title = {On advantages of the Kelvin mapping in finite element + implementations of deformation processes}, + journal = {Environmental Earth Sciences}, + year = {2016}, + volume = {75}, + number = {11}, + pages = {937} +} + +@article{Dellinger1998, + author = {Dellinger, J. and Vasicek, D. and Sondergeld, C.}, + title = {Kelvin notation for stabilizing elastic-constant inversion}, + journal = {Revue de l'Institut Fran{\c{c}}ais du P{\'e}trole}, + year = {1998}, + volume = {53}, + number = {5}, + pages = {709--719}, + url = {http://sepwww.stanford.edu/oldsep/joe/Reprints/8IWSA.pdf}, +} + diff --git a/include/deal.II/algorithms/general_data_storage.h b/include/deal.II/algorithms/general_data_storage.h index e4cc5cda6f..cf6f9c989c 100644 --- a/include/deal.II/algorithms/general_data_storage.h +++ b/include/deal.II/algorithms/general_data_storage.h @@ -36,19 +36,7 @@ DEAL_II_NAMESPACE_OPEN * It offers a mechanism to store any amount of data, of any type, * which is then made accessible by an identifier string. * - * When using this class, please cite - * - * @code{.bib} - * @article{SartoriGiulianiBardelloni-2018-a, - * Author = {Sartori, Alberto and Giuliani, Nicola and - * Bardelloni, Mauro and Heltai, Luca}, - * Journal = {SoftwareX}, - * Pages = {318--327}, - * Title = {{deal2lkit: A toolkit library for high performance - * programming in deal.II}}, - * Volume = {7}, - * Year = {2018}} - * @endcode + * When using this class, please cite @cite SartoriGiulianiBardelloni-2018-a. */ class GeneralDataStorage : public Subscriptor { diff --git a/include/deal.II/base/parsed_convergence_table.h b/include/deal.II/base/parsed_convergence_table.h index 9b2dc59d04..64b852a10a 100644 --- a/include/deal.II/base/parsed_convergence_table.h +++ b/include/deal.II/base/parsed_convergence_table.h @@ -118,19 +118,7 @@ class ParameterHandler; * set Rate mode = reduction_rate_log2 * @endcode * - * When using this class, please cite - * @code{.bib} - * @article{SartoriGiulianiBardelloni-2018-a, - * Author = {Sartori, Alberto and Giuliani, Nicola and - * Bardelloni, Mauro and Heltai, Luca}, - * Journal = {SoftwareX}, - * Pages = {318--327}, - * Title = {{deal2lkit: A toolkit library for high performance - * programming in deal.II}}, - * Doi = {10.1016/j.softx.2018.09.004}, - * Volume = {7}, - * Year = {2018}} - * @endcode + * When using this class, please cite @cite SartoriGiulianiBardelloni-2018-a. */ class ParsedConvergenceTable { diff --git a/include/deal.II/base/symmetric_tensor.h b/include/deal.II/base/symmetric_tensor.h index 8fe43abc0f..3fcccf0132 100644 --- a/include/deal.II/base/symmetric_tensor.h +++ b/include/deal.II/base/symmetric_tensor.h @@ -2938,35 +2938,9 @@ namespace internal { /** * Tridiagonalize a rank-2 symmetric tensor using the Householder method. - * The specialized algorithm implemented here is given in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * The specialized algorithm implemented here is given in @cite Kopp2008 * and is based off of the generic algorithm presented in section 11.3.2 of - * @code{.bib} - * @book{Press2007, - * title = {Numerical recipes 3rd edition: The art of scientific - * computing}, - * author = {Press, W. H.}, - * journal = {Cambridge university press}, - * year = {2007} - * } - * @endcode + * @cite Press2007. * * @param[in] A This tensor to be tridiagonalized * @param[out] Q The orthogonal matrix effecting the transformation @@ -2985,35 +2959,9 @@ namespace internal /** * Compute the eigenvalues and eigenvectors of a real-valued rank-2 * symmetric tensor using the QL algorithm with implicit shifts. - * The specialized algorithm implemented here is given in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * The specialized algorithm implemented here is given in @cite Kopp2008 * and is based off of the generic algorithm presented in section 11.4.3 of - * @code{.bib} - * @book{Press2007, - * title = {Numerical recipes 3rd edition: The art of scientific - * computing}, - * author = {Press, W. H.}, - * journal = {Cambridge university press}, - * year = {2007} - * } - * @endcode + * @cite Press2007. * * @param[in] A The tensor of which the eigenvectors and eigenvalues are * to be computed. @@ -3030,35 +2978,9 @@ namespace internal /** * Compute the eigenvalues and eigenvectors of a real-valued rank-2 * symmetric tensor using the Jacobi algorithm. - * The specialized algorithm implemented here is given in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * The specialized algorithm implemented here is given in @cite Kopp2008 * and is based off of the generic algorithm presented in section 11.4.3 of - * @code{.bib} - * @book{Press2007, - * title = {Numerical recipes 3rd edition: The art of scientific - * computing}, - * author = {Press, W. H.}, - * journal = {Cambridge university press}, - * year = {2007} - * } - * @endcode + * @cite Press2007. * * @param[in] A The tensor of which the eigenvectors and eigenvalues are * to be computed. @@ -3097,25 +3019,7 @@ namespace internal * eigenvalues and an analytical approach based on the cross-product for the * eigenvectors. If the computations are deemed too inaccurate then the * method falls back to ql_implicit_shifts. The specialized algorithm - * implemented here is given in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * implemented here is given in @cite Kopp2008. * * @param[in] A The tensor of which the eigenvectors and eigenvalues are * to be computed. @@ -3159,25 +3063,7 @@ namespace internal * SymmetricTensor objects. * * The specialized algorithms utilized in computing the eigenvectors are - * presented in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * presented in @cite Kopp2008. */ enum struct SymmetricTensorEigenvectorMethod { @@ -3219,25 +3105,7 @@ enum struct SymmetricTensorEigenvectorMethod * is sorted in descending order (determined by the eigenvalues). * * The specialized algorithms utilized in computing the eigenvectors are - * presented in - * @code{.bib} - * @article{Kopp2008, - * title = {Efficient numerical diagonalization of hermitian 3x3 - * matrices}, - * author = {Kopp, J.}, - * journal = {International Journal of Modern Physics C}, - * year = {2008}, - * volume = {19}, - * number = {3}, - * pages = {523--548}, - * doi = {10.1142/S0129183108012303}, - * eprinttype = {arXiv}, - * eprint = {physics/0610206v3}, - * eprintclass = {physics.comp-ph}, - * url = - * {https://www.mpi-hd.mpg.de/personalhomes/globes/3x3/index.html} - * } - * @endcode + * presented in @cite Kopp2008. * * @relatesalso SymmetricTensor */ diff --git a/include/deal.II/fe/fe_bernardi_raugel.h b/include/deal.II/fe/fe_bernardi_raugel.h index 71d912bdcc..c9d7cf8665 100644 --- a/include/deal.II/fe/fe_bernardi_raugel.h +++ b/include/deal.II/fe/fe_bernardi_raugel.h @@ -44,21 +44,7 @@ DEAL_II_NAMESPACE_OPEN * pressure space to provide additional accuracy commensurate with the * cost of the large number of velocity unknowns. * - * The element was introduced in the following paper: - * @code{.bib} - * @article{BR85, - * author = {Christine Bernardi and Genevi{\`e}ve Raugel}, - * title = {Analysis of some finite elements for the {S}tokes problem}, - * journal = {Mathematics of Computation}, - * publisher = {American Mathematical Society ({AMS})}, - * volume = {44}, - * number = {169}, - * pages = {71--79}, - * year = {1985}, - * doi = {10.1090/s0025-5718-1985-0771031-7}, - * url = {https://doi.org/10.1090/s0025-5718-1985-0771031-7} - * } - * @endcode + * The element was introduced in the paper @cite BR85. * * *

Degrees of freedom

diff --git a/include/deal.II/lac/qr.h b/include/deal.II/lac/qr.h index fc7405d746..8a4d48e157 100644 --- a/include/deal.II/lac/qr.h +++ b/include/deal.II/lac/qr.h @@ -193,46 +193,8 @@ protected: * to have basic operations such as additions, scalar product, etc. * It also needs to have a copy-constructor. * - * See sections 6.5.2-6.5.3 on pp. 335-338 in - * @code{.bib} - * @Book{Golub2013, - * title = {Matrix computations}, - * publisher = {Johns Hopkins University Press}, - * year = {2013}, - * author = {Golub, Gene H and Van Loan, Charles F}, - * edition = {4}, - * } - * @endcode - * as well as - * @code{.bib} - * @article{Daniel1976, - * author = {Daniel, James W and Gragg, Walter Bill and Kaufman, Linda and Stewart, Gilbert W}, - * title = {{Reorthogonalization and stable algorithms for updating the Gram-Schmidt QR factorization}}, - * journal = {Mathematics of Computation}, - * year = {1976}, - * volume = {30}, - * number = {136}, - * pages = {772--795}, - * } - * @Article{Reichel1990, - * author = {Reichel, L. and Gragg, W. B.}, - * title = {{Algorithm 686: FORTRAN Subroutines for Updating the QR Decomposition}}, - * journal = {ACM Trans. Math. Softw.}, - * year = {1990}, - * volume = {16}, - * number = {4}, - * pages = {369--377}, - * month = dec, - * issn = {0098-3500}, - * acmid = {98291}, - * address = {New York, NY, USA}, - * doi = {10.1145/98267.98291}, - * issue_date = {Dec. 1990}, - * numpages = {9}, - * publisher = {ACM}, - * url = {http://doi.acm.org/10.1145/98267.98291}, - * } - * @endcode + * See sections 6.5.2-6.5.3 on pp. 335-338 in @cite Golub2013 as well as + * @cite Daniel1976 and @cite Reichel1990. */ // clang-format on template diff --git a/include/deal.II/lac/utilities.h b/include/deal.II/lac/utilities.h index 2f6f9ccaa1..67e0e386dc 100644 --- a/include/deal.II/lac/utilities.h +++ b/include/deal.II/lac/utilities.h @@ -108,19 +108,7 @@ namespace Utilities * OperatorType has to provide vmult operation with * VectorType. * - * This function implements the algorithm from - * @code{.bib} - * @article{Zhou2006, - * Title = {Self-consistent-field Calculations Using Chebyshev-filtered - * Subspace Iteration}, - * Author = {Zhou, Yunkai and Saad, Yousef and Tiago, Murilo L. and - * Chelikowsky, James R.}, - * Journal = {Journal of Computational Physics}, - * Year = {2006}, - * Volume = {219}, - * Pages = {172--184}, - * } - * @endcode + * This function implements the algorithm from @cite Zhou2006. * * @note This function uses Lapack routines to compute the largest * eigenvalue of $T_k$. @@ -167,18 +155,7 @@ namespace Utilities * @p vector_memory is used to allocate memory for temporary objects. * * This function implements the algorithm (with a minor fix of sign of - * $\sigma_1$) from - * @code{.bib} - * @article{Zhou2014, - * Title = {Chebyshev-filtered subspace iteration method free of sparse - * diagonalization for solving the Kohn--Sham equation}, - * Author = {Zhou, Yunkai and Chelikowsky, James R and Saad, Yousef}, - * Journal = {Journal of Computational Physics}, - * Year = {2014}, - * Volume = {274}, - * Pages = {770--782}, - * } - * @endcode + * $\sigma_1$) from @cite Zhou2014. * * @note If @p tau is equal to * std::numeric_limits::infinity(), no normalization diff --git a/include/deal.II/meshworker/scratch_data.h b/include/deal.II/meshworker/scratch_data.h index b518c8d171..6c34c744e5 100644 --- a/include/deal.II/meshworker/scratch_data.h +++ b/include/deal.II/meshworker/scratch_data.h @@ -203,19 +203,7 @@ namespace MeshWorker * } * @endcode * - * When using this class, please cite - * @code{.bib} - * @article{SartoriGiulianiBardelloni-2018-a, - * Author = {Sartori, Alberto and Giuliani, Nicola and - * Bardelloni, Mauro and Heltai, Luca}, - * Journal = {SoftwareX}, - * Pages = {318--327}, - * Title = {{deal2lkit: A toolkit library for high performance - * programming in deal.II}}, - * Doi = {10.1016/j.softx.2018.09.004}, - * Volume = {7}, - * Year = {2018}} - * @endcode + * When using this class, please cite @cite SartoriGiulianiBardelloni-2018-a. */ template class ScratchData diff --git a/include/deal.II/optimization/line_minimization.h b/include/deal.II/optimization/line_minimization.h index 1747d23376..30dcd3ce78 100644 --- a/include/deal.II/optimization/line_minimization.h +++ b/include/deal.II/optimization/line_minimization.h @@ -147,27 +147,8 @@ namespace LineMinimization * signature. * * The function implements Algorithms 2.6.2 and 2.6.4 on pages 34-35 in - * @code{.bib} - * @book{Fletcher2013, - * title = {Practical methods of optimization}, - * publisher = {John Wiley \& Sons}, - * year = {2013}, - * author = {Fletcher, Roger}, - * isbn = {978-0-471-49463-8}, - * doi = {10.1002/9781118723203}, - * } - * @endcode - * These are minor variations of Algorithms 3.5 and 3.6 on pages 60-61 in - * @code{.bib} - * @book{Nocedal2006, - * title = {Numerical Optimization}, - * publisher = {Springer New York}, - * year = {2006}, - * author = {Jorge Nocedal and S. Wright}, - * address = {233 Spring Street, New York, NY 10013, USA}, - * doi = {10.1007/978-0-387-40065-5}, - * } - * @endcode + * @cite Fletcher2013. These are minor variations of Algorithms 3.5 + * and 3.6 on pages 60-61 in @cite Nocedal2006. * It consists of a bracketing phase and a zoom phase, where @p interpolate is used. * * Two examples of use might be as follows: diff --git a/include/deal.II/physics/notation.h b/include/deal.II/physics/notation.h index fd6ab5096b..df94dfbf1a 100644 --- a/include/deal.II/physics/notation.h +++ b/include/deal.II/physics/notation.h @@ -247,33 +247,7 @@ namespace Physics * include no such factors. * * Some useful references that show how this notation works include, amongst - * others, - * @code{.bib} - * @article{Nagel2016, - * author = {Nagel, T. and G{\"o}rke, U-J. and Moerman, K. and Kolditz, - * O.}, - * title = {On advantages of the Kelvin mapping in finite element - * implementations of deformation processes}, - * journal = {Environmental Earth Sciences}, - * year = {2016}, - * volume = {75}, - * number = {11}, - * pages = {937} - * } - * @endcode - * and - * @code{.bib} - * @article{Dellinger1998, - * author = {Dellinger, J. and Vasicek, D. and Sondergeld, C.}, - * title = {Kelvin notation for stabilizing elastic-constant inversion}, - * journal = {Revue de l'Institut Fran{\c{c}}ais du P{\'e}trole}, - * year = {1998}, - * volume = {53}, - * number = {5}, - * pages = {709--719}, - * url = {http://sepwww.stanford.edu/oldsep/joe/Reprints/8IWSA.pdf}, - * } - * @endcode + * others, @cite Nagel2016 and @cite Dellinger1998 * as well as the online reference found on * this -- 2.39.5