February 2014 - firedrake - imperial.ac.uk

Periodic Table of the Finite Elements poster
by Florian Rathgeber 13 Feb '14

13 Feb '14

This may be of interest to some: Anders, Douglas Arnold and Mattias Schläger are looking for feedback on a poster of a Periodic Table of the Finite Elements they have been working on before it goes to print: https://bitbucket.org/fenics-project/dolfin/wiki/Periodic%20Table%20of%20th… Florian

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This week's FEM lecture is Friday 1030-1200
by David Ham 11 Feb '14

11 Feb '14

Greetings all, with a little more notice than last week, this week's lecture will be 1030-1200 in WPL 3.01. We'll be looking at techniques for nonlinear problems, and working up towards boundary condition implementation. Regards, David -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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talk today at 12 on multithreading in games
by Kelly, Paul H J 11 Feb '14

11 Feb '14

Thought you might find this interesting: http://www.doc.ic.ac.uk/cpp/aci_talks/?event=23

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Another snazzy red chair
by Kelly, Paul H J 07 Feb '14

07 Feb '14

We are invited to grab the remaining snazzy red chair from wpl212. It might get thrown out otherwise. It is a two person job - go for it! Paul

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Intel talk on the future of memory systems architecture
by Kelly, Paul H J 07 Feb '14

07 Feb '14

Further to my comments from my visit to AMD about the future of memory systems, you might like to have a look at these slides from Intel: http://hpcadvisorycouncil.com/events/2014/stanford-workshop/presentations/d… Maybe in particular slides 17-22. This is from an Exascale meeting at Stanford this week, http://hpcadvisorycouncil.com/events/2014/stanford-workshop/agenda.php Best wishes Paul

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Re: [firedrake] This week's FEM lecture is Friday 1030-1200
by David Ham 06 Feb '14

06 Feb '14

Greetings all, Humble apologies for this slipping me by. There will indeed be a FEM lecture tomorrow 1030-1200. We're going to look at actual assembly of left and right hand side integrals using quadrature. Regards, David On 30 January 2014 16:59, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > Greetings all, > > A small reminder that this week's lectures will be tomorrow at 1030. > > Regards, > > David > > > On 28 January 2014 12:06, David Ham <David.Ham(a)imperial.ac.uk> wrote: > >> Dear all, >> >> This week's FEM lecture will be on Friday from 1030-1200 in WPL3.01 as >> usual. This week we'll be venturing out into the world of FEM in more than >> one dimension! >> >> Regards, >> >> David >> >> -- >> Dr David Ham >> Departments of Mathematics and Computing >> Imperial College London >> >> http://www.imperial.ac.uk/people/david.ham >> > > > > -- > Dr David Ham > Departments of Mathematics and Computing > Imperial College London > > http://www.imperial.ac.uk/people/david.ham > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Boundary conditions
by David Ham 02 Feb '14

02 Feb '14

Standard GMSH problem: if you have a physical line you also need a physical surface or GMSH will drop all the interior elements from the output. On Saturday, February 1, 2014, Cotter, Colin J <colin.cotter(a)imperial.ac.uk> wrote: > Dear Firedrakers, > I decided to create another set of cohomology tests, this time with > Dirichlet boundary conditions, since there is a nice result relating the > kernels of the operators with and without Dirichlet boundary conditions > (for the maths-curious, it's Poincare duality). > > However, I can't get the boundary tags into Firedrake from gmsh. If I > attempt to tag the boundary using "Physical Line" in gmsh (see bottom of > this email for the .geo file), the line > >>mesh = Mesh("annulus.msh") > produces: > *** ERROR *** > Error message: Unsupported mixture of face/element types > > Removing the physical line makes the error message go away, so there is > something wrong with that line. > > What have I done wrong? > > all the best > --Colin > > Point(1) = {0, 0, 0, 1.0}; > Point(2) = {1, 0, 0, 1.0}; > Point(3) = {1, 1, 0, 1.0}; > Point(4) = {0, 1, 0, 1.0}; > Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; > Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; > Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; > Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; > Line(1) = {1, 2}; > Line(2) = {2, 3}; > Line(3) = {3, 4}; > Line(4) = {4, 1}; > Line(5) = {5, 6}; > Line(6) = {6, 7}; > Line(7) = {7, 8}; > Line(8) = {8, 5}; > Line Loop(1) = {1, 2, 3, 4}; > Line Loop(2) = {5, 6, 7, 8}; > Plane Surface(1) = {1,2}; > Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5}; > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Boundary conditions
by David Ham 02 Feb '14

02 Feb '14

mymatrix = assemble(myform, bcs=bcs) mymatrix.assemble() # Force the delayed assembly. mymatrix.M.values # Numpy array. On 2 February 2014 09:04, Cotter, Colin J <colin.cotter(a)imperial.ac.uk>wrote: > OK, next question is whether I can output a numpy matrix for a bilinear > form assembled with boundary conditions, i.e. whether I can get the reduced > matrix with the boundary rows and columns removed? > > I can see that the bcs are postponed until the solve, so if this exists it > would just be a utility for testing. If it doesn't I can remove them myself. > > --cjc > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Cotter, Colin J [colin.cotter(a)imperial.ac.uk] > *Sent:* 02 February 2014 08:54 > > *To:* firedrake > *Subject:* Re: [firedrake] Boundary conditions > > Ah good, works, thanks. > > --cjc > ------------------------------ > *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:* 01 February 2014 22:12 > *To:* firedrake > *Subject:* Re: [firedrake] Boundary conditions > > Standard GMSH problem: if you have a physical line you also need a > physical surface or GMSH will drop all the interior elements from the > output. > > On Saturday, February 1, 2014, Cotter, Colin J < > colin.cotter(a)imperial.ac.uk> wrote: > >> Dear Firedrakers, >> I decided to create another set of cohomology tests, this time with >> Dirichlet boundary conditions, since there is a nice result relating the >> kernels of the operators with and without Dirichlet boundary conditions >> (for the maths-curious, it's Poincare duality). >> >> However, I can't get the boundary tags into Firedrake from gmsh. If I >> attempt to tag the boundary using "Physical Line" in gmsh (see bottom of >> this email for the .geo file), the line >> >>mesh = Mesh("annulus.msh") >> produces: >> *** ERROR *** >> Error message: Unsupported mixture of face/element types >> >> Removing the physical line makes the error message go away, so there is >> something wrong with that line. >> >> What have I done wrong? >> >> all the best >> --Colin >> >> Point(1) = {0, 0, 0, 1.0}; >> Point(2) = {1, 0, 0, 1.0}; >> Point(3) = {1, 1, 0, 1.0}; >> Point(4) = {0, 1, 0, 1.0}; >> Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; >> Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; >> Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; >> Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; >> Line(1) = {1, 2}; >> Line(2) = {2, 3}; >> Line(3) = {3, 4}; >> Line(4) = {4, 1}; >> Line(5) = {5, 6}; >> Line(6) = {6, 7}; >> Line(7) = {7, 8}; >> Line(8) = {8, 5}; >> Line Loop(1) = {1, 2, 3, 4}; >> Line Loop(2) = {5, 6, 7, 8}; >> Plane Surface(1) = {1,2}; >> Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5}; >> >> > > -- > Dr David Ham > Departments of Mathematics and Computing > Imperial College London > > http://www.imperial.ac.uk/people/david.ham > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Boundary conditions
by Cotter, Colin J 01 Feb '14

01 Feb '14

Dear Firedrakers, I decided to create another set of cohomology tests, this time with Dirichlet boundary conditions, since there is a nice result relating the kernels of the operators with and without Dirichlet boundary conditions (for the maths-curious, it's Poincare duality). However, I can't get the boundary tags into Firedrake from gmsh. If I attempt to tag the boundary using "Physical Line" in gmsh (see bottom of this email for the .geo file), the line >>mesh = Mesh("annulus.msh") produces: *** ERROR *** Error message: Unsupported mixture of face/element types Removing the physical line makes the error message go away, so there is something wrong with that line. What have I done wrong? all the best --Colin Point(1) = {0, 0, 0, 1.0}; Point(2) = {1, 0, 0, 1.0}; Point(3) = {1, 1, 0, 1.0}; Point(4) = {0, 1, 0, 1.0}; Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 1}; Line(5) = {5, 6}; Line(6) = {6, 7}; Line(7) = {7, 8}; Line(8) = {8, 5}; Line Loop(1) = {1, 2, 3, 4}; Line Loop(2) = {5, 6, 7, 8}; Plane Surface(1) = {1,2}; Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5};

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PyOP2 installation
by Cotter, Colin J 01 Feb '14

01 Feb '14

Dear all, I just installed the forked FFC/UFL/etc. on my laptop using pip install --user. I presume that I need to add these to my pythonpath, what is not clear is which actual directory needs to be added? Is it .local/lib/site-packages? cheers --cjc

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