fluidsim merge requestshttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests2019-11-20T14:11:48Zhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/107Fix issues opened by Jason2019-11-20T14:11:48ZBitbucket ImporterFix issues opened by Jason*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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* get\_field\_to\_...*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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* get\_field\_to\_plot returns \(field, time\)
* black
* init\_with\_initialized\_state called in load\_state\_phys\_file
* Improve error messages in phys\_fields3d plot
https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/1060.3.22019-11-14T14:02:12ZBitbucket Importer0.3.2*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/105Default2020-02-12T22:50:08ZBitbucket ImporterDefault*Created originally on Bitbucket by [Jason Reneuve](https://bitbucket.org/%7B729768e9-4f6b-40bf-802c-062cfecca79b%7D/)*
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* fixed bugs in examples/int...*Created originally on Bitbucket by [Jason Reneuve](https://bitbucket.org/%7B729768e9-4f6b-40bf-802c-062cfecca79b%7D/)*
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* fixed bugs in examples/internal\_waves\_coriolis/simul\_ns3dstrat\_waves.py
* fixed a bug in operators.operators3d.OperatorsPseudoSpectral3D.urudfft\_from\_vxvyfft
* black
* changed confusing variable name in operators.operators3d.OperatorsPseudoSpectral3D.urudfft\_from\_vxvyfft
https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/104Fix a bug in examples/internal_waves_coriolis/simul_ns3dstrat_waves.py2020-02-12T22:50:07ZBitbucket ImporterFix a bug in examples/internal_waves_coriolis/simul_ns3dstrat_waves.py*Created originally on Bitbucket by [Jason Reneuve](https://bitbucket.org/%7B729768e9-4f6b-40bf-802c-062cfecca79b%7D/)*
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*Created originally on Bitbucket by [Jason Reneuve](https://bitbucket.org/%7B729768e9-4f6b-40bf-802c-062cfecca79b%7D/)*
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https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/103New max_elapsed parameter2019-07-15T12:20:50ZBitbucket ImporterNew max_elapsed parameter*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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* Start to impleme...*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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* Start to implement a max\_elapsed parameter
* Tests and example for params.time\_stepping.max\_elapsedhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/102Improvements function plots in modules spectra and spectral energy budget2019-06-13T12:02:08ZBitbucket ImporterImprovements function plots in modules spectra and spectral energy budget*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Improvement method ...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Improvement method \_get\_concatenate\_data in spatio\_temporal\_spectra.py.
* Translation scaling k\*\*-3 with argument level3.
* Correction title Spectral energy budget.
* Remove total spectra \+ add Ozmidov.https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/101Warning for pkgload2019-04-30T13:37:09ZBitbucket ImporterWarning for pkgload*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was auto...*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was automatically generatedhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/100Hyperlinks in rst2019-04-30T13:37:28ZBitbucket ImporterHyperlinks in rst*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was auto...*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was automatically generatedhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/99Bibtex and __citation__2019-04-30T08:16:52ZBitbucket ImporterBibtex and __citation__*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was auto...*Created originally on Bitbucket by [avmo (Ashwin Vishnu)](https://bitbucket.org/%7Bbd72905e-cf99-4847-84c2-998104370f6e%7D/)*
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This request was automatically generatedhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/98Avoid bug restart frequency_spectra.py2019-04-05T18:12:50ZBitbucket ImporterAvoid bug restart frequency_spectra.py*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Plot instantaneous ...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Plot instantaneous kxkz spectra function plot.
* Avoid bugs restart frequency\_spectra.py \+ function \_concatenate\_data.
* Black.https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/97Use Transonic 0.2.02019-03-15T09:54:51ZBitbucket ImporterUse Transonic 0.2.0*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/96Remove check one direction in fluidsim/base/forcing/anisotropic.py.2019-03-13T22:28:08ZBitbucket ImporterRemove check one direction in fluidsim/base/forcing/anisotropic.py.*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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No need check one dir...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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No need check one direction.
There is a check if self.nb\_forced\_modes == 0 in fluidsim/base/forcing/specific.pyhttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/95Importable module find_dissipation + black2020-02-12T22:49:55ZBitbucket ImporterImportable module find_dissipation + black*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Decrease markersize...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Decrease markersize inset plot \+ title.
* Add band forcing region function plot.
* Fixed band function plot spect\_energy\_budget.
* Function load\_mean for module find\_dissipation.
* New module find\_dissipation.
* Fixed plot forcing band spectra.
* Importable module find\_dissipation \+ black.https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/94Setup appveyor + version 0.3.12019-03-10T05:56:51ZBitbucket ImporterSetup appveyor + version 0.3.1*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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First release whic...*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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First release which should work on Windowshttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/93Default2019-03-05T16:39:30ZBitbucket ImporterDefault*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Fix sorted in \_get...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Fix sorted in \_get\_concatenate\_data.
* Add function inset plot spectral space with forcing region.
* Add buoyancy scale in spect\_energy\_budget and spectrahttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/92Stop using Cython (pseudo_spect_cy.pyx)2019-03-04T21:06:24ZBitbucket ImporterStop using Cython (pseudo_spect_cy.pyx)*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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It should fix this...*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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It should fix this problem [https://bitbucket.org/fluiddyn/fluidsim/issues/28/installing-fluidsim-in-miniconda3-on](https://bitbucket.org/fluiddyn/fluidsim/issues/28/installing-fluidsim-in-miniconda3-on)
A Cython extension was built but it wasn’t used any longer by default.
This PR makes fluidsim a pure Python code \(with bits compiled by Transonic / Pythran\).
It decreases the installation and maintenance issues.
It’s going to be easier to improve our time stepping code.
Without Pythran, it leads to a small performance reduction, but anyway, for performance, Fluidsim needs Pythran.https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/91Mention the papers in the doc2019-03-01T07:20:22ZBitbucket ImporterMention the papers in the doc*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/90Default2020-02-12T22:49:50ZBitbucket ImporterDefault*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Improve string name...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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* Improve string name run \+ add compute forcing\_rate in normalization \+ add docstrings.
* Improve compute omega\_af \+ f-strings name\_run.https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/89Fix memory leak allreduce in increments2020-02-12T22:49:49ZBitbucket ImporterFix memory leak allreduce in increments*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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Fixes issue #29 \(...*Created originally on Bitbucket by [paugier (Pierre Augier)](https://bitbucket.org/%7Beb327c54-cadd-4fce-9edd-f8fe047a9b93%7D/)*
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Fixes issue #29 \(for CPython 3.7.0 and 3.7.1\).
Note that other uses of allreduce are for integers and it seems that there is no memory leak in this case \(or very small\). Anyway, this problem has been solved in CPython 3.7.2, so I don’t think it’s worth it to do much more on this problem.
The main memory leak was for increments and it should be solved with this PR. We know that there should be another similar case in fluidfft, which could be fixed the same way, but another strategy would be to use CPython == 3.6 or >= 3.7.2.
* Fix memory leak allreduce \+ simul\_ns2dstrat\_quasi1d.py
* Improve strat/outputshttps://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/88Add function plot_kz_omega_cross_section in test_solver.py.2019-02-22T15:47:15ZBitbucket ImporterAdd function plot_kz_omega_cross_section in test_solver.py.*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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Add function plot\_kz...*Created originally on Bitbucket by [calpe (Miguel Calpe)](https://bitbucket.org/%7B3a110e54-047d-4a20-bfc6-0f16d9ecf7a6%7D/)*
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Add function plot\_kz\_omega\_cross\_section\(\) in test\_solver.py
Coverage = 94% \(spatio\_temporal\_spectra.py\)