February 2019 - firedrake - imperial.ac.uk

Re: [firedrake] local stuff in UFL
by Lawrence Mitchell 09 Mar '19

09 Mar '19

> On 28 Feb 2019, at 10:36, Cotter, Colin J <colin.cotter(a)imperial.ac.uk> wrote: > > Thanks! > > I also need to stop pullbacks from being applied, how do I do that? > > What we actually need is to be able to replace J uhat/det J with J P(uhat)/det J where > P is the projection onto a vector in local coordinates, probably it is easiest to just hand > write the whole expression as it should appear after pullback. I you write everything after pullback, you might be able to get away with editing tsfc/ufl_utils.py to set do_apply_function_pullbacks=False. I'm hope that will work. Lawrence

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local stuff in UFL
by Cotter, Colin J 28 Feb '19

28 Feb '19

Dear Firedrakers, With Toyo Sadare we are looking at implementing a new type of lumping scheme to remove the spectral gap from the RT2-DG1 (Norwegian numbering) spaces for linear shallow water on quadrilaterals. To implement this we need to be able to write some stuff in local coordinates instead of global, including defining coefficients that are functions of local coordinate (stuff like xi_1(1-xi_1) etc.). What is the best way to do this? all the best --cjc

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Re: [firedrake] miklos.eu nachricht
by Nishida Knapp 18 Feb '19

18 Feb '19

Sehr geehrte Frau, sehr geehrter Herr, Wir sind froh, Ihnen mitteilen zu dürfen das der DomainName miklos.eu zur möglichen Abgabe steht. Würden Sie mir bitte eine kurze Rückmeldung geben ob es für Sie von Interesse ist? Ich wünsche einen guten Start in die neue Woche. Nishida Knapp

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Issues compiling on Lustre filesystem
by Jon Hill 08 Feb '19

08 Feb '19

Hi folks, I'm having issues compiling on York's new supercomputer (Viking - cool name). I have successfully compiled on the machine, but in the frontend /users space which is not available on the backend. When I compile on he backend filesystem, I get the error attached - basically a permission error when moving files The drive available on the backend is called scratch. I've tried a few things: - move the venv: virtualenv --relocatable firedrake, mv it, but this fails when running (just hangs somewhere in the simulation - probably mpipy) These all fail compilation: - set the TMPDIR flag to /user during compilation - compile on the back end - compile on the frontend directly on /scratch I suspect it's something to do with the Lustre filesystem as I can compile on the frontend space. Thanks in advance for any advice! Jon -- Dr Jon Hill Senior Lecturer in Physical Geography Department of Environment and Geography University of York M: +44(0)7748254812 P: +44(0)1904 324480 Twitter: @jonxhill Web: https://jonxhill.wordpress.com/ Web: https://envmodellinggroup.github.io/

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Failing to install on remote workstation
by Gibson, Thomas 08 Feb '19

08 Feb '19

Hi all, I’m attempting to install Firedrake on a remote Ubuntu workstation. Unfortunately I have not been successful. I’m not quite sure what I need to do to fix this. I have attached the log with this email. Best regards, - Thomas

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Re: [firedrake] installation problem
by Ham, David A 08 Feb '19

08 Feb '19

Dear Junho, The Firedrake install failed. The issue appears to be that your python was built without ssl. This breaks installing various packages that we depend on. You need to talk to your local sysadmins about why your Python ssl is broken. If they can’t fix this for you, it is fairly straightforward to build python from source and use that. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "(대학원생) 최준호 (수리과학과)" <freedom(a)unist.ac.kr> Date: Friday, 8 February 2019 at 12:15 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] installation problem Dear firedrake manager, I failed to install the firedrake even though I reinstalled python latest and firedrake. python3 and firedrake seem to run well. But when I ran "the Simple Helmholtz equation" on introductory tutorials, "NameError: name 'UnitSquareMesh' is not defined" appeared. Would you help me? Thank you for the help you can provide. Regards, Junho

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installation problem
by (대학원생) 최준호 (수리과학과) 08 Feb '19

08 Feb '19

Dear firedrake manager, I failed to install the firedrake even though I reinstalled python latest and firedrake. python3 and firedrake seem to run well. But when I ran "the Simple Helmholtz equation" on introductory tutorials, "NameError: name 'UnitSquareMesh' is not defined" appeared. Would you help me? Thank you for the help you can provide. Regards, Junho

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Solving BVPs on periodic meshes
by Shrimali, Bhavesh 08 Feb '19

08 Feb '19

Hello, Is it possible in firedrake to solve a BVP with periodic BCs on conforming meshes (symmetric nodes on opposite faces in case of a cubic unit cell)? I have a unit cell with random microstructure and a correpsonding periodic mesh at my disposal (generated from Netgen: https://ngsolve.org/) in Gmsh2 (.msh) format. Netgen/NGSolve<https://ngsolve.org/> Netgen/NGSolve is a high performance multiphysics finite element software. It is widely used to analyze models from solid mechanics, fluid dynamics and electromagnetics. ngsolve.org I am looking for something similar to https://fenicsproject.org/docs/dolfin/1.4.0/python/demo/documented/periodic… except with the mesh instead of being a plain-unit square (cube) is a unit square (cube) with a bunch of holes inside. Is there a minimal example on how to crete subclasses just like it is done above in dolfin (demo_periodic.py), or otherwise, to illustrate implementation of Periodic BCs?

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Re: [firedrake] Interpolating/projecting between meshes
by Ham, David A 02 Feb '19

02 Feb '19

Dear Peter, We don’t have nodal evaluation for arbitrary finite elements. The interpolation operator (both interpolate and Function.at) works for spaces with point evaluation nodes i.e. CG and DG so you can rig up a hack by interpolating the RT field into the spanning DG field (which is lossless), interpolating that into a spanning DG field on the new mesh (you can get the coordinates to interpolate at by interpolating the coordinate field into the corresponding vector DG space), and then finally projecting from the DG space down to RT. This is effectively a variant on: https://www.firedrakeproject.org/interpolation.html#interpolation-from-exte… However a nicer approach is probably to use Patrick Farrell’s pefarrell/supermesh-mixed-mass-matrix branch which makes project work between different meshes of the same domain. Finally, I notice you are using C string expressions. We’re about to drop that functionality because it’s superceded by UFL expressions. E.g. x = SpatialCoordinate(mesh) interpolate(u, as_vector(x[0] + 1, x[1]) Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Sentz, Peter" <sentz2(a)illinois.edu> Date: Thursday, 31 January 2019 at 22:41 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] Interpolating/projecting between meshes Hello, In Fenics/Dolfin, I can interpolate between different meshes, even with less basic elements like Raviart-Thomas. For example: from fenics import * mesh1 = UnitSquareMesh(1,1) mesh2 = UnitSquareMesh(2,2) V1 = FunctionSpace(mesh1,'RT',1) V2 = FunctionSpace(mesh2,'RT',1) u = Expression(('x[0] + 1','x[1]'),degree = 1) U = interpolate(u,V1) Uf = interpolate(U,V2) Interpolating the function 'U' that is defined on one mesh can be moved to another in a fairly simple matter. Trying something similar in Firedrake with 'project' instead of 'interpolate' results in an error message. A different error appears for nodal FE functions as well, when using 'interpolate'. However, in that case, I have developed a work-around using mesh.coordinates.dat.data. However, I can't see how to extend this to nodal DG or Raviart-Thomas FE functions. Can you access the coordinates of the degrees of freedom of an arbitrary function space? Barring that, is there some mechanism to move between meshes if I use a MeshHierarchy, for example? Thanks, Peter Sentz

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Does anybody have experience of installing on RedHat?
by David Colling 01 Feb '19

01 Feb '19

Hi, I am trying to install Firedrake on RedHat Fedoraand am having all sorts of wows. Does anybody have experience of doing this or a recipe that I can try? Best, david

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