import petsc4py
import sys
petsc4py.init(sys.argv)
from petsc4py import PETSc
__all__ = ["Citations"]
[docs]
class Citations(dict):
"""Entry point to citations management.
This singleton object may be used to record Bibtex citation
information and then register that a particular citation is
relevant for a particular computation. It hooks up with PETSc's
citation registration mechanism, so that running with
``-citations`` does the right thing.
Example usage::
Citations().add("key", "bibtex-entry-for-my-funky-method")
...
if using_funky_method:
Citations().register("key")
"""
_instance = None
def __new__(cls):
if cls._instance is None:
cls._instance = super(Citations, cls).__new__(cls)
return cls._instance
[docs]
def add(self, key, entry):
"""Add a paper to the database of possible citations.
:arg key: The key to use.
:arg entry: The bibtex entry.
"""
self[key] = entry
[docs]
def register(self, key):
"""Register a paper to be cited so that PETSc knows about it.
:arg key: The key of the relevant citation.
:raises: :exc:`KeyError` if no such citation is
found in the database.
Papers to be cited can be added using :meth:`add`.
.. note::
The intended use is that :meth:`register` should be called
only when the referenced functionality is actually being
used.
"""
cite = self.get(key, None)
if cite is None:
raise KeyError("Did not find a citation for '%s', did you forget to add it?" % key)
PETSc.Sys.registerCitation(cite)
[docs]
@classmethod
def print_at_exit(cls):
"""Print citations when exiting."""
# We devolve to PETSc for actually printing citations.
PETSc.Options()["citations"] = None
Citations().add("Rathgeber2016", """
@Article{Rathgeber2016,
author = {Florian Rathgeber and David A. Ham and Lawrence
Mitchell and Michael Lange and Fabio Luporini and
Andrew T. T. McRae and Gheorghe-Teodor Bercea and
Graham R. Markall and Paul H. J. Kelly},
title = {Firedrake: automating the finite element method by
composing abstractions},
journal = {ACM Trans. Math. Softw.},
year = 2016,
volume = {43},
number = {3},
year = {2016},
issn = {0098-3500},
pages = {24:1--24:27},
doi = {10.1145/2998441},
archiveprefix ={arXiv},
eprint = {1501.01809},
url = {http://arxiv.org/abs/1501.01809}
}
""")
Citations().add("McRae2016", """
@Article{McRae2016,
author = {Andrew T. T. McRae and Gheorghe-Teodor Bercea and
Lawrence Mitchell and David A. Ham and Colin
J. Cotter},
title = {Automated generation and symbolic manipulation of
tensor product finite elements},
journal = {SIAM Journal on Scientific Computing},
year = 2016,
volume = 38,
number = 5,
pages = {S25--S47},
doi = {10.1137/15M1021167},
archiveprefix ={arXiv},
eprint = {1411.2940},
primaryclass = {math.NA},
url = {http://arxiv.org/abs/1411.2940}
}
""")
Citations().add("Homolya2016", """
@Article{Homolya2016,
author = {Mikl\'os Homolya and David A. Ham},
title = {A parallel edge orientation algorithm for
quadrilateral meshes},
journal = {SIAM Journal on Scientific Computing},
year = 2016,
volume = 38,
number = 5,
pages = {S48--S61},
doi = {10.1137/15M1021325},
archiveprefix ={arXiv},
eprint = {1505.03357},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1505.03357}
}
""")
Citations().add("Luporini2015", """
@Article{Luporini2015,
author = {Fabio Luporini and Ana Lucia Varbanescu and Florian
Rathgeber and Gheorghe-Teodor Bercea and
J. Ramanujam and David A. Ham and Paul H. J. Kelly},
title = {Cross-Loop Optimization of Arithmetic Intensity for
Finite Element Local Assembly},
journal = {ACM Transactions on Architecture and Code
Optimization},
year = 2015,
volume = 11,
number = 4,
pages = {57:1--57:25},
url = {http://doi.acm.org/10.1145/2687415},
doi = {10.1145/2687415},
}
""")
Citations().add("Luporini2016", """
@article{Luporini2016,
author = {Fabio Luporini and David A. Ham and Paul H. J. Kelly},
title = {An algorithm for the optimization of finite element
integration loops},
journal = {ACM Transactions on Mathematical Software},
year = 2017,
volume = 44,
issue = 1,
pages = {3:1--3:26},
archiveprefix ={arXiv},
eprint = {1604.05872},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1604.05872},
doi = {10.1145/3054944},
}
""")
Citations().add("Bercea2016", """
@Article{Bercea2016,
author = {Gheorghe{-}Teodor Bercea and Andrew T. T. McRae and
David A. Ham and Lawrence Mitchell and Florian
Rathgeber and Luigi Nardi and Fabio Luporini and
Paul H. J. Kelly},
title = {A structure-exploiting numbering algorithm for
finite elements on extruded meshes, and its
performance evaluation in Firedrake},
journal = {Geoscientific Model Development},
year = 2016,
volume = 9,
number = 10,
pages = {3803--3815},
doi = {10.5194/gmd-9-3803-2016},
archiveprefix ={arXiv},
eprint = {1604.05937},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1604.05937}
}
""")
Citations().add("Mitchell2016", """
@Article{Mitchell2016,
author = {Lawrence Mitchell and Eike Hermann M\"uller},
title = {High level implementation of geometric multigrid
solvers for finite element problems: applications in
atmospheric modelling},
journal = {Journal of Computational Physics},
year = 2016,
volume = 327,
pages = {1--18},
doi = {10.1016/j.jcp.2016.09.037},
archiveprefix ={arXiv},
eprint = {1605.00492},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1605.00492}
}
""")
Citations().add("Homolya2017", """
@Misc{Homolya2017,
author = {Mikl\'os Homolya and Lawrence Mitchell and Fabio Luporini and
David A. Ham},
title = {{TSFC: a structure-preserving form compiler}},
year = 2017,
archiveprefix = {arXiv},
eprint = {1705.03667},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1705.003667}
}
""")
Citations().add("Kirby2017", """
@Article{Kirby2017,
author = {Robert C. Kirby and Lawrence Mitchell},
title = {{Solver composition across the PDE/linear algebra
barrier}},
journal = {SIAM Journal on Scientific Computing},
year = 2018,
volume = 40,
number = 1,
pages = {C76-C98},
doi = {10.1137/17M1133208},
archiveprefix ={arXiv},
eprint = {1706.01346},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1706.01346}
}
""")
Citations().add("Homolya2017a", """
@Misc{Homolya2017a,
author = {Mikl\'os Homolya and Robert C. Kirby and David
A. Ham},
title = {{Exposing and exploiting structure: optimal code
generation for high-order finite element methods}},
year = 2017,
archiveprefix ={arXiv},
eprint = {1711.02473},
primaryclass = {cs.MS},
url = {http://arxiv.org/abs/1711.02473}
}
""")
Citations().add("Gibson2018", """
@Misc{Gibson2018,
author = {Thomas H. Gibson and Lawrence Mitchell and David
A. Ham and Colin J. Cotter},
title = {{A domain-specific language for the hybridization
and static condensation of finite element methods}},
year = 2018,
archiveprefix ={arXiv},
eprint = {1802.00303},
primaryclass = {cs.MS},
url = {https://arxiv.org/abs/1802.00303}
}
""")
Citations().add("Kolev2009", """
@Misc{Kolev2009,
author = {Kolev, Tzanio V and Vassilevski, Panayot S},
title = {{Parallel auxiliary space AMG for H (curl) problems}},
journal = {Journal of Computational Mathematics},
year = 2009,
volume = 27,
number = 5,
pages = {604--623},
url = {https://www.jstor.org/stable/43693530}
}
""")
Citations().add("Hiptmair1998", """
@Misc{Hiptmair1998,
author = {Hiptmair, Ralf},
title = {{Multigrid Method for Maxwell's Equations}},
journal = {SIAM Journal on Numerical Analysis},
volume = {36},
number = {1},
pages = {204-225},
year = {1998},
doi = {10.1137/S0036142997326203},
url = {https://doi.org/10.1137/S0036142997326203},
}
""")
Citations().add("nixonhill2023consistent", """
@article{nixonhill2023consistent,
author = {Nixon-Hill, R. W. and Shapero, D. and Cotter, C. J. and Ham, D. A.},
doi = {10.5194/gmd-17-5369-2024},
journal = {Geoscientific Model Development},
number = {13},
pages = {5369--5386},
title = {Consistent point data assimilation in Firedrake and Icepack},
url = {https://gmd.copernicus.org/articles/17/5369/2024/},
volume = {17},
year = {2024}
}
""")
Citations().add("FiredrakeUserManual", """
@manual{FiredrakeUserManual,
author = {David A. Ham and Paul H. J. Kelly and Lawrence
Mitchell and Colin J. Cotter and Robert C. Kirby and Koki Sagiyama and
Nacime Bouziani and Sophia Vorderwuelbecke and Thomas J. Gregory and
Jack Betteridge and Daniel R. Shapero and Reuben W. Nixon-Hill and
Connor J. Ward and Patrick E. Farrell and Pablo D. Brubeck and India
Marsden and Thomas H. Gibson and Miklós Homolya and Tianjiao Sun and
Andrew T. T. McRae and Fabio Luporini and Alastair Gregory and
Michael Lange and Simon W. Funke and Florian Rathgeber and
Gheorghe-Teodor Bercea and Graham R. Markall},
doi = {10.25561/104839},
edition = {First edition},
month = {5},
organization = {Imperial College London and University of Oxford and
Baylor University and University of Washington},
title = {Firedrake User Manual},
year = {2023}
}
""")
Citations().add("Bouziani2021", """
@article{Bouziani2021,
title={Escaping the abstraction: a foreign function interface for the {Unified} {Form} {Language} {[UFL]}},
author={Bouziani, Nacime and Ham, David A},
journal = {{Differentiable} {Programming} {Workshop} at {NeurIPS} 2021},
url = {http://arxiv.org/abs/2111.00945},
note = {arXiv: 2111.00945},
year={2021}
}
""")
Citations().add("Bouziani2023", """
@inproceedings{Bouziani2023,
title = {Physics-driven machine learning models coupling {PyTorch} and {Firedrake}},
author = {Bouziani, Nacime and Ham, David A.},
booktitle = {{ICLR} 2023 {Workshop} on {Physics} for {Machine} {Learning}},
year = {2023},
doi = {10.48550/arXiv.2303.06871}
}
""")
Citations().add("Bouziani2024", """
@article{Bouziani2024,
title = {Differentiable programming across the {PDE} and {Machine} {Learning} barrier},
author = {Bouziani, Nacime and Ham, David A. and Farsi, Ado},
journal = {arXiv preprint arXiv:2409.06085},
eprint = {2409.06085},
url = {https://arxiv.org/abs/2409.06085},
year = {2024}
}
""")
Citations().add("Betteridge2024", """
@article{Betteridge2024,
doi = {10.21105/joss.07359},
url = {https://doi.org/10.21105/joss.07359},
year = {2024},
publisher = {The Open Journal},
volume = {9},
number = {104},
pages = {7359},
author = {Jack Betteridge and Patrick E. Farrell and Matthias Hochsteger
and Christopher Lackner and Joachim Schöberl and Stefano Zampini
and Umberto Zerbinati},
title = {ngsPETSc: A coupling between NETGEN/NGSolve and PETSc},
journal = {Journal of Open Source Software} }
""")
