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periodic boundary conditions?
by Lawrence Mitchell 07 May '16

07 May '16

This message reached me as a list administrator from Francis Poulin (but I couldn't figure out how to release it onto the list, so instead, it's copied below). Lawrence Hello, Glad to see the posters are looking great. Sorry that I won't get to see them in person this year but glad I could contribute a little. Hopefully I'll get to attend next year with a grad student. I have a question on how to convert the QG code from a channel to periodic boundary conditions. You can find a demo version of the code at https://github.com/francispoulin/firedrake/blob/qg_demo/demos/quasigeostrop… I have removed the jet and only have random initial conditions. The good news is that 2D turbulence does happen and structures merge but in a channel. To reproduce classical results I would like it to be doubly periodic. I made two changes: 1) I asked it to be periodic in this line by switching "x" to "both". mesh = PeriodicRectangleMesh(n0, n0, Lx, Ly, direction="both", quadrilateral=True, reorder=None ) 2) We should not impose Dirichlet boundary conditions. To do this I removed bcs=bc1 in the following psi_problem = LinearVariationalProblem(Apsi,Lpsi,psi0) It occurs to me that perhaps one needs to explicitly impose periodic boundary conditions. Is that the case? If yes then do I need to change the following somehow? bc1 = [DirichletBC(Vcg, 0., 1 ), DirichletBC(Vcg, 0., 2 )] When I run the code it does run but it doesn't converge (after 42 steps) and dies. This is for the same resolution and everything else that does converge for the channel case. Could it be that the periodic case is not as well conditioned if it is periodic in both directions? I hope to make a nice simulation of this to see the structures merging and increasing in size. What's really nice is that if I wanted to do 3D turbulence in the context of 3D the changes are pretty small. I need to define the grid to be 3D and impose Neumann BCs at the top and bottom. That I will ask about at a later time. Cheers, Francis ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637

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Re: [firedrake] periodic boundary conditions?
by Colin Cotter 07 May '16

07 May '16

Hi Francis, In our setup, periodic boundary conditions are not really boundary conditions, they are just a property of the mesh topology. So, the solver should not have any bc passed in. If the Helmholtz solve has failed, most probably it is because the simulation blew up due to CFL constraint violation, and then garbage was passed in to the Helmholtz solver. You should check that and maybe reduce the timestep if necessary. all the best --cjc On 7 May 2016 at 16:41, Mitchell, Lawrence <lawrence.mitchell(a)imperial.ac.uk > wrote: > This message reached me as a list administrator from Francis Poulin (but I > couldn't figure out how to release it onto the list, so instead, it's > copied below). > > Lawrence > > > Hello, > > Glad to see the posters are looking great. Sorry that I won't get to see > them in person this year but glad I could contribute a little. Hopefully > I'll get to attend next year with a grad student. > > I have a question on how to convert the QG code from a channel to periodic > boundary conditions. You can find a demo version of the code at > > > https://github.com/francispoulin/firedrake/blob/qg_demo/demos/quasigeostrop… > > I have removed the jet and only have random initial conditions. > > The good news is that 2D turbulence does happen and structures merge but > in a channel. To reproduce classical results I would like it to be doubly > periodic. > > I made two changes: > > 1) I asked it to be periodic in this line by switching "x" to "both". > > mesh = PeriodicRectangleMesh(n0, n0, Lx, Ly, direction="both", > quadrilateral=True, reorder=None > ) > > > 2) We should not impose Dirichlet boundary conditions. To do this I > removed bcs=bc1 in the following > > psi_problem = > LinearVariationalProblem(Apsi,Lpsi,psi0) > > > It occurs to me that perhaps one needs to explicitly impose periodic > boundary conditions. Is that the case? If yes then do I need to change > the following somehow? > > bc1 = [DirichletBC(Vcg, 0., 1 > ), > DirichletBC(Vcg, > 0., 2 > )] > > > When I run the code it does run but it doesn't converge (after 42 steps) > and dies. This is for the same resolution and everything else that does > converge for the channel case. Could it be that the periodic case is not > as well conditioned if it is periodic in both directions? > > I hope to make a nice simulation of this to see the structures merging and > increasing in size. > > What's really nice is that if I wanted to do 3D turbulence in the context > of 3D the changes are pretty small. I need to define the grid to be 3D and > impose Neumann BCs at the top and bottom. That I will ask about at a later > time. > > Cheers, Francis > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] gmsh mesh loading error
by Lawrence Mitchell 06 May '16

06 May '16

Dear Tomasz, Please note, you get much better responses (faster) if you send mail to the firedrake list, rather than me individually. > On 6 May 2016, at 16:19, Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> wrote: > [0] DMPlexCreateGmsh() line 247 in /tmp/pip-5Zhs5M-build/src/dm/impls/plex/plexgmsh.c > [0] Invalid argument > [0] Could not determine Plex facet for element 2241 > > Yet, if I comment the next to last line in the .geo file, then it runs. I have no understanding of the intricacies of the Gmsh file format, or indeed what it does. However, your geo file appears not to be using the Transfinite Volume command correctly.

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Abstractions poster
by David Ham 06 May '16

06 May '16

Greetings Firedrakers, Poster number two is now up at: http://www.doc.ic.ac.uk/~dham/abstractions.pdf This is a revision of the abstractions poster to take into account developments over the last year or so - especially TSFC. It also has Andrew's new institution on it. This is a candidate final draft so please check it for obvious cockups. Cheers, David

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Re: [firedrake] vector function point-wise initialisation
by Colin Cotter 06 May '16

06 May '16

Dear TJ, It isn't really intended that you get direct access to basis coefficients like this in Firedrake, and even if the grid is structured there is no particular order in which you can expect the basis coefficients to appear. The best plan is to subclass Expression and give it an eval method that takes in the coordinates of a point and returns the value (you will need to search your array for this), as documented here: http://firedrakeproject.org/interpolation.html#python-expression-classes This will not be very efficient but does the job. all the best --cjc On 5 May 2016 at 18:52, Sun, Tianjiao <tianjiao.sun14(a)imperial.ac.uk> wrote: > Thanks Colin. > > What I was trying to set up is an image, so nx and ny are the number of > pixels in each direction (I'm trying a pretty simplistic formulation as you > can see...) The function g here will be things like the image gradient > function, which I have only the numerical values but not the expression. > > So I guess my question is how to get topological information about basis > functions, in particular, for a rectangular mesh with degree 1 Lagrange > element, are the basis functions arranged in a specific order? (so that I > can use something like g.vector().set_local() to set the values). > > Many thanks, > -TJ > > > On 05/05/16 18:34, Colin Cotter wrote: > > Dear TJ, > If you want to initialise from a known function then you should do this > by interpolating an Expression into a Function. Note that your mesh > initialisation is probably not what you intended either, please check the > doc-string for RectangleMesh. > > all the best > --cjc > > On 5 May 2016 at 18:31, Sun, Tianjiao <tianjiao.sun14(a)imperial.ac.uk> > wrote: > >> Dear team, >> >> I have a beginner question about function initialisation in Firedrake. >> >> I have the follow simple mesh and function space, and I want to >> initialise function g with values from numpy arrays (gx, gy). I'm not >> sure which way should I align the data in the constructor, i.e. should I >> concatenate gx, gy or interleave them? >> >> mesh = RectangleMesh(nx-1,ny-1,nx,ny) >> V = VectorFunctionSpace(mesh, "CG", 1) >> >> # g = Function(V, np.concatenate((gx, gy), axis=0))) ??? >> >> Many thanks, >> -TJ >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > > > > -- > http://www.imperial.ac.uk/people/colin.cotter > > www.cambridge.org/9781107663916 > > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] vector function point-wise initialisation
by Colin Cotter 05 May '16

05 May '16

Dear TJ, If you want to initialise from a known function then you should do this by interpolating an Expression into a Function. Note that your mesh initialisation is probably not what you intended either, please check the doc-string for RectangleMesh. all the best --cjc On 5 May 2016 at 18:31, Sun, Tianjiao <tianjiao.sun14(a)imperial.ac.uk> wrote: > Dear team, > > I have a beginner question about function initialisation in Firedrake. > > I have the follow simple mesh and function space, and I want to > initialise function g with values from numpy arrays (gx, gy). I'm not > sure which way should I align the data in the constructor, i.e. should I > concatenate gx, gy or interleave them? > > mesh = RectangleMesh(nx-1,ny-1,nx,ny) > V = VectorFunctionSpace(mesh, "CG", 1) > > # g = Function(V, np.concatenate((gx, gy), axis=0))) ??? > > Many thanks, > -TJ > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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vector function point-wise initialisation
by Tianjiao Sun 05 May '16

05 May '16

Dear team, I have a beginner question about function initialisation in Firedrake. I have the follow simple mesh and function space, and I want to initialise function g with values from numpy arrays (gx, gy). I'm not sure which way should I align the data in the constructor, i.e. should I concatenate gx, gy or interleave them? mesh = RectangleMesh(nx-1,ny-1,nx,ny) V = VectorFunctionSpace(mesh, "CG", 1) # g = Function(V, np.concatenate((gx, gy), axis=0))) ??? Many thanks, -TJ

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Applications poster
by David Ham 05 May '16

05 May '16

Dear Firedrakers, Thanks for your input to the applications poster. A draft is now up at: http://www.doc.ic.ac.uk/~dham/applications.pdf I had to edit down some headings and text, so check what I have written. I am happy to change it - as long as the number of characters stays essentially constant. As you can see, the logos ended up on a darker background, so I have two particular requests: Anna, can you please send me the reversed colour Leeds logo. I think you need a Leeds login to get it. Similarly, Justin can you please send be the reversed color Houston text logo. It's at: http://www.uh.edu/policies/graphic-standards/download-zone/

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Archer
by Colin Cotter 05 May '16

05 May '16

Dear all, My Archer renewal came through, meaning I need to start using my AUs before they take them away again! What is the status of the Archer Firedrake build? Is there anything I can do to help? cheers --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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[IMUM 2016] Second Announcement and Call for Papers
by Lawrence Mitchell 04 May '16

04 May '16

Dear all, some of you (ocean modellers?) may be interested in the following workshop in the south of France in September. Cheers, Lawrence -------- Forwarded Message -------- Subject: [IMUM 2016] Second Announcement and Call for Papers Date: Wed, 4 May 2016 17:06:52 +0200 From: Contact Imum <contact.imum2016(a)gmail.com> . We are pleased to announce the *15th IMUM international workshop* that will take place in *Toulouse, 27-30 September 2016*. It will be hosted by L'Observatoire Midi-Pyrénées <http://www.obs-mip.fr/>and LEGOS Ocean Science Laboratory <http://www.legos.obs-mip.fr/>. The three first days of the workshop (Tuesday 27th to Thursday 29th) will be dedicated to conventional scientific presentations (oral/posters) and discussions. The last day of the workshop (Sept. 30) will be dedicated for software demos and/or the exchange of numerical tools among participants (software market place) on an informal basis. Presentations (oral or poster formats) may address any aspect of unstructured-mesh modeling of coastal, shelf, and global systems. In 2016, we especially encourage submissions addressing: * next-generation multi-scale models, from unstructured to structured (and intermediate) approaches, including nesting * vertical coordinates and optimal horizontal/vertical grid design * modelling of the shoreline-continental shelf-ocean continuum However, we welcome a broad scope of presentations, ranging from unstructured-mesh model applications and inter-comparison to advances in finite volume or finite element discretization, high-order schemes, pre-conditioners, solvers, distributed computing, mesh generators, adaptive modeling, data assimilation, coupling across physical, sediment and biogeochemical models, etc. We also welcome contributions providing objective comparisons between structured and unstructured-mesh models and more generally describing numerical benchmarks. Information on the workshop, including registration and abstract submission, can be found at https://imum2016.sciencesconf.org/. _Important deadlines:_ **Abstract submission June 10 2016* **Early Registration discount July 15 2016* Before submitting an abstract pleaseregister <https://imum2016.sciencesconf.org/registration/index>for the workshop. Once registered, don't forget to submit registration fees <https://www.azur-colloque.fr/DR14/AzurInscription/?&iColId=62&NaiveForm_id=…> before July 15th to obtain the early registration discount. After that date, all fees will increase from 250 euros (students 150 euros) to 300 euros. We look forward to seeing you at this dynamic workshop. Florent Lyard contact.imum2016(a)gmail.com <mailto:contact.imum2016@gmail.com> <http://imum_2016.sciencesconf.org/> https://imum2016.sciencesconf.org/

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