February 2017 - firedrake - imperial.ac.uk

Re: [firedrake] square root of matrix
by Colin Cotter 15 Feb '17

15 Feb '17

Hi Francis, Actually taking the sqrt of the Laplacian matrix doesn't give you the right thing for SQG, because the mass matrix is involved. If you want to do SQG with finite elements you really have to mesh the 3D domain and solve the 3D Poisson equation on that, and extract the surface values. all the best --cjc On 14 February 2017 at 15:47, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello Colin, > > I don't have an answer to your question but I am very curious to know if > someone else. > > In the Surface QG model, to determine the streamfunction from the buoyancy > you need to solve an equation that looks like > > b = - (Laplacian)^1/2 \psi > > What people typically do is to transform everything into spectral space > where it then becomes > > \hat b = - K \hat \psi > > It requires using FFT's, which are easily accessible, but I'm not sure if > this is relevant to the problem you want to solve. > > If someone figures out how to do this in Firedrake I would be happy to add > another SQG demo, since it would only require a minor change from the > existing QG code. > > 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 <(519)%20888-4567> > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Colin Cotter [colin.cotter(a)imperial.ac.uk] > *Sent:* Tuesday, February 14, 2017 3:21 AM > *To:* firedrake > *Subject:* [firedrake] square root of matrix > > Dear all, > For weird reasons I'd like to solve Ux = y where U is the Cholesky > square root of a given symmetric positive definite matrix A. Is there a way > to abuse the PETSc solver interface into doing this? > > all the best > --cjc > > -- > http://www.imperial.ac.uk/people/colin.cotter > > www.cambridge.org/9781107663916 > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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square root of matrix
by Colin Cotter 14 Feb '17

14 Feb '17

Dear all, For weird reasons I'd like to solve Ux = y where U is the Cholesky square root of a given symmetric positive definite matrix A. Is there a way to abuse the PETSc solver interface into doing this? all the best --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Prescribe pressure at a corner for Darcy's equation
by David Ham 13 Feb '17

13 Feb '17

Hi Justin, This is expected behaviour. Your attempt to impose a pressure BC using: dot(w,n)*patm*ds(6) will do nothing in the no-flow condition because the no-flow condition restricts the test space to the space for which dot(w, n) = 0. Your surface integral therefore contributes nothing to the form. I'm not even sure that the Stokes equations admit simultaneously specifying no flow and a fixed pressure. Intuitively, the no flow condition implies that the pressure rises at the boundary to the level required such that the pressure gradient normal to the boundary is zero and no flow results. Regards, David On Mon, 13 Feb 2017 at 07:25 Justin Chang <jychang48(a)gmail.com> wrote: > Hi again, > > So this may or may not be related to the original issue. I was able to > define corner IDs needed for my pressure BCs but I cannot seem to enforce > both no-flow and atmospheric pressure simultaneously. Enforcing no-flow > seems to negate the weakly prescribed pressure flux and my pressure > solution is complete wack. On the otherhand, not enforcing no flow gives me > a pressure profile I expect, but I no longer have a no flow domain. > > Attached is my code, the custom boundary IDs begin at line 39, the weak > formulations begin at line 164. Run the code as: > > python 2D_Darcy_Homo_Iso.py 600 150 2 > > The code right now will generate a nonsensical pressure solution because I > have no-flow enforced on all boundaries (including the corners). > > Any ideas on what to do here? > > Thanks, > Justin > > On Tue, Feb 7, 2017 at 4:55 AM, Lawrence Mitchell < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > On 7 Feb 2017, at 09:03, Lawrence Mitchell < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > > > PETSc.Options("foo_").getAll() > > > > => {"bar": "-baz_bar"} > > > > I will push a fix for this one. > > Please try the branch proposed here: > > https://github.com/firedrakeproject/firedrake/pull/1004 > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- Dr David Ham Department of Mathematics Imperial College London

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Prescribe pressure at a corner for Darcy's equation
by Justin Chang 13 Feb '17

13 Feb '17

Hi all, I am trying to simulate the 2D benchmark Elder problem, which is density-driven fluid flow in porous media. The problem is essentially Darcy's equation where no flow boundary conditions are enforced on all four sides (let's suppose the computational domain is 600m by 150m). To ensure uniqueness, pressure is prescribed at the top left and top right corners. Suppose I want to use the RT0 formulation. If my pressure is non-zero, how would I prescribe if I were to use one of the built-in Mesh functions (as opposed to GMSH)? I know for RT0, the pressure bc is prescribed weakly but how do I literally only have the two element faces that connect each of the top left and top right corners apply said boundary condition? Thanks, Justin

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Firedrake users and developers meeting dealines FRIDAY.
by David Ham 09 Feb '17

09 Feb '17

Hi All, Just a little poke to remind you that the abstract and early registration deadline for Firedrake '17 is this Friday. Links for both are available via the workshop page: http://firedrakeproject.org/firedrake_17.html Regards, David -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Firedrake user and developer workshop -- 27 & 28 March 2017
by David Ham 07 Feb '17

07 Feb '17

Hi All, Sorry, I hadn't realised I'd spammed the whole list with that mail! The simple answer is that Imperial is in a very touristy area so there are tonnes of hotels. Just typing Imperial College London into, for example, expedia turns up very many within a short walk. This is, unfortunately, a very expensive area but we hope you'll appreciate our effort to make your trip more affordable by devaluing the pound by 20% ;). Justin: the hotel Matt pointed you to is also, I'm sure, just fine. It's on the other side of the park so it's a little further away, but you get a nice walk across Kensington Gardens. Regards, David On Tue, 7 Feb 2017 at 16:59 Julian Andrej <juan(a)tf.uni-kiel.de> wrote: > I don't know if its recommended but i at the Best Western Hebron, > which is 15minutes from the location and reasonably priced. > > On Tue, Feb 7, 2017 at 5:29 PM, Justin Chang <jychang48(a)gmail.com> wrote: > > I am also wondering the same thing regarding where to stay. Knepley > tells me > > Hilton Hyde Park is one place. Is that recommended? > > > > On Tue, Feb 7, 2017 at 10:24 AM Francis Poulin <fpoulin(a)uwaterloo.ca> > wrote: > >> > >> Hello, > >> > >> Yes, I still am. I even have an abstract that I plan to submit later > >> today. Sorry for my tardiness. I will probably submit it this evening > my > >> time. > >> > >> Does anyone have any advice as to where would be convenient to stay? > It's > >> been a decade since I've been to London and sadly have never visited > >> Imperial. I am looking forward to it. > >> > >> > >> 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 <(519)%20888-4567> > >> > >> From: firedrake-bounces(a)imperial.ac.uk [ > firedrake-bounces(a)imperial.ac.uk] > >> on behalf of David Ham [David.Ham(a)imperial.ac.uk] > >> Sent: Tuesday, February 07, 2017 4:36 AM > >> To: firedrake > >> Subject: Re: [firedrake] Firedrake user and developer workshop -- 27 & > 28 > >> March 2017 > >> > >> Hi Francis, > >> > >> Thanks for your ongoing support for Firedrake. I was wondering if you > were > >> still thinking of coming to Firedrake '17. > >> > >> Regards, > >> > >> David > >> > >> On Tue, 15 Nov 2016 at 15:41 Francis Poulin <fpoulin(a)uwaterloo.ca> > wrote: > >>> > >>> Hello David, > >>> > >>> This sounds great! I will most certainly try to attend and hopefully > >>> bring a grad student along. > >>> > >>> I am also happy to help if I can and look forward to meeting everyone > in > >>> person. > >>> > >>> 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 <(519)%20888-4567> > >>> > >>> ________________________________ > >>> From: firedrake-bounces(a)imperial.ac.uk [ > firedrake-bounces(a)imperial.ac.uk] > >>> on behalf of David Ham [David.Ham(a)imperial.ac.uk] > >>> Sent: Tuesday, November 15, 2016 5:59 AM > >>> To: firedrake > >>> Subject: [firedrake] Firedrake user and developer workshop -- 27 & 28 > >>> March 2017 > >>> > >>> Dear Firedrakers, > >>> > >>> The first Firedrake user and developer workshop will be held on 27 & 28 > >>> March 2017 at Imperial College London. Please save the dates! > >>> > >>> The Firedrake workshop will provide the opportunity for Firedrake users > >>> and developers to engage with each other to communicate the ways that > >>> Firedrake can be used in simulation science, the latest developments > in the > >>> project, and the future developments anticipated. The workshop will > >>> incorporate a half day Firedrake tutorial for interested new users, > and will > >>> present more experienced users with the opportunity to spend face to > face > >>> time with developers and other users. > >>> > >>> A call for contributions and registration information will be published > >>> in a few weeks. I hope to see many of you there. > >>> > >>> Regards, > >>> > >>> David > >> > >> -- > >> Dr David Ham > >> Department of Mathematics > >> Imperial College London > >> _______________________________________________ > >> firedrake mailing list > >> firedrake(a)imperial.ac.uk > >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Firedrake user and developer workshop -- 27 & 28 March 2017
by David Ham 07 Feb '17

07 Feb '17

Hi Francis, Thanks for your ongoing support for Firedrake. I was wondering if you were still thinking of coming to Firedrake '17. Regards, David On Tue, 15 Nov 2016 at 15:41 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello David, > > This sounds great! I will most certainly try to attend and hopefully > bring a grad student along. > > I am also happy to help if I can and look forward to meeting everyone in > person. > > 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 <(519)%20888-4567> > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of David Ham [David.Ham(a)imperial.ac.uk] > *Sent:* Tuesday, November 15, 2016 5:59 AM > *To:* firedrake > *Subject:* [firedrake] Firedrake user and developer workshop -- 27 & 28 > March 2017 > > Dear Firedrakers, > > The first Firedrake user and developer workshop will be held on 27 & 28 > March 2017 at Imperial College London. Please save the dates! > > The Firedrake workshop will provide the opportunity for Firedrake users > and developers to engage with each other to communicate the ways that > Firedrake can be used in simulation science, the latest developments in the > project, and the future developments anticipated. The workshop will > incorporate a half day Firedrake tutorial for interested new users, and > will present more experienced users with the opportunity to spend face to > face time with developers and other users. > > A call for contributions and registration information will be published in > a few weeks. I hope to see many of you there. > > Regards, > > David > -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Firedrake and xcode
by David Ham 07 Feb '17

07 Feb '17

Hi Francis, If you are able to give this a try this would be great. We don't currently have a clean Mac lying around to try this on. Regards, David On Thu, 2 Feb 2017 at 16:06 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello David, > > Thanks for looking into this detail. Is this something that you might > want me to try and see if the installation works? > > 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 <(519)%20888-4567> > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of David Ham [David.Ham(a)imperial.ac.uk] > *Sent:* Wednesday, February 01, 2017 5:28 AM > *To:* firedrake > *Subject:* Re: [firedrake] Firedrake and xcode > > Hi Francis, > > We're basically installing xcode in order to have the compilers. I wasn't > aware until this week that you could get the compilers by just installing > the much smaller xcode command line tools. It's entirely possible that this > is sufficient, but we (or someone) would need to test this. I think one > just needs to comment out lines 955 to 958 of firedrake-install and then > try running it on a clean Mac. > > Regards, > > David > > On Tue, 31 Jan 2017 at 16:42 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > > Hello, > > I have had several students install Firedrake on a MacMini and each time > the full version of Xcode needed to be installed. Is this necessarily the > case? If yes, what in particular is needed? > > 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 <(519)%20888-4567> > > -- > Dr David Ham > Department of Mathematics > Imperial College London > -- Dr David Ham Department of Mathematics Imperial College London

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High-contrast Stokes problem
by Loic Gouarin 06 Feb '17

06 Feb '17

Hi, I would like to solve a Stokes problem with a viscosity which is not constant and could be high in some parts of the domain (as in sinker problem). The solvers that I want to use are in this article: http://dx.doi.org.ezproxy.math.cnrs.fr/10.1016/j.cam.2013.10.016 I would like to use a P0 interpolation for the viscosity function. Could you tell me how can I set this function into my variational formulation ? The other question is to construct the S matrix when you use the Schur complement as a preconditioner. I have to set the pressure mass matrix for S and scale it with the inverse of the viscosity. How can I do that ? Thanks, Loic -- Tel: 01 69 15 60 14 http://www.math.u-psud.fr/~gouarin https://github.com/gouarin

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Re: [firedrake] Firedrake and xcode
by David Ham 02 Feb '17

02 Feb '17

Hi Francis, We're basically installing xcode in order to have the compilers. I wasn't aware until this week that you could get the compilers by just installing the much smaller xcode command line tools. It's entirely possible that this is sufficient, but we (or someone) would need to test this. I think one just needs to comment out lines 955 to 958 of firedrake-install and then try running it on a clean Mac. Regards, David On Tue, 31 Jan 2017 at 16:42 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > I have had several students install Firedrake on a MacMini and each time > the full version of Xcode needed to be installed. Is this necessarily the > case? If yes, what in particular is needed? > > 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 <(519)%20888-4567> > > -- Dr David Ham Department of Mathematics Imperial College London

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