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},
+}
+
* 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
{
* 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
{
{
/**
* 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
/**
* 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.
/**
* 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.
* 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.
* 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
{
* 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
*/
* 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.
*
*
* <h3>Degrees of freedom</h3>
* 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 <typename VectorType>
* OperatorType has to provide <code>vmult</code> 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 $T_k$.
* @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
* <code>std::numeric_limits<double>::infinity()</code>, no normalization
* }
* @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 <int dim, int spacedim = dim>
class ScratchData
* 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:
* 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
* <a
* href="https://en.wikipedia.org/wiki/Voigt_notation#Mandel_notation">this
projects / dealii.git / commitdiff