October 2015 - firedrake - imperial.ac.uk

Inverse of .dat.data
by Buesing, Henrik 30 Oct '15

30 Oct '15

Dear all, Ok. Maybe this is the way to go: As before, I have a function temp(p,h), which shall return temperature dependent on pressure and enthalpy. I insert UFL representations of p and h into temp(,). Then I'm doing a p = assemble(p).dat.data[0] h = assemble(h).dat.data[1] Now, I execute some operations on the arrays. In the end I want to have the UFL representation of temp (the same as what I inserted as p and h). So how do I get the UFL representation back from the array? Thank you! Henrik -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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Re: [firedrake] Higher order bendy
by Andrew McRae 30 Oct '15

30 Oct '15

Yes. The simple idea of 1) building a higher-order (vector-valued) Function 2) setting its values appropriately 3) setting mesh.coordinates = new_coordinates does _not_ "just work", because UFL manages to sniff the function space of the something of the domain [you get the idea] that the coordinate field Function was built on. This, of course, is still P1/Q1. Therefore the generated C code is written as if the coordinate field is still lowest-order. I've recently discovered that simply doing mesh.coordinates = new_coordinates seems to break many things, including Firedrake par_loops and mixed problems. I understand Miklós has made significant progress on a more robust solution. If you're desperately trying to get something working in time for Monday(!), there might be a short-term hack that makes sure the underlying coordinates are (e.g.) quadratic and builds everything on top of that, but I don't remember the details. On 29 October 2015 at 21:14, Colin Cotter <colin.cotter(a)imperial.ac.uk> wrote: > Hi all, > Please can you remind me what the story is with higher order coordinate > fields? Do I recall correctly that there is a snag? > Cheers Cjc >

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Higher order bendy
by Colin Cotter 29 Oct '15

29 Oct '15

Hi all, Please can you remind me what the story is with higher order coordinate fields? Do I recall correctly that there is a snag? Cheers Cjc

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New Firedrake dependency - libspatialindex
by Homolya, Miklós 29 Oct '15

29 Oct '15

Dear Firedrake users, the latest update adds a new dependency to Firedrake: libspatialindex. (Ubuntu package name: libspatialindex-dev; Homebrew name: spatialindex) The install script is updated accordingly, so fresh installs should just work, however, updates might fail. You may just install the package manually before updating, or you could rebuild the update script: http://firedrakeproject.org/download.html#recovering-from-a-broken-installa… Best regards, Miklós

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Re: [firedrake] Issues with Firedrake
by David Ham 28 Oct '15

28 Oct '15

It's slightly hard to tell since you didn't include the .geo file, however it appears that you are still using strings to label boundaries. Note that 114 is an integer but "114" is a string. Regards, David On Wed, 28 Oct 2015 at 12:44 William Booker <scwb(a)leeds.ac.uk> wrote: > > > I seem to be misunderstanding something as I'm still getting the invalid > gmsh file error. How would I label the edges in the mesh file? > > Will > ------------------------------ > *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:* 22 October 2015 16:32 > *To:* firedrake > *Subject:* Re: [firedrake] Issues with Firedrake > > Aha. After a little experimentation, it turns out that PETSc does not > support gmsh Physical Lines labelled with strings. If you replace the > strings with (unique) numbers then it will work. This appears to be an > upstream issue with PETSc. > > Regards, > > David > > On Thu, 22 Oct 2015 at 10:24 William Booker <scwb(a)leeds.ac.uk> wrote: > >> Dear Firedrakers, >> >> I fixed the physical name issue from last time but I'm still getting that >> the msh file isn't valid. What can I do to correct this? >> >> Thanks in advance, >> >> Will >> >> >> ------------------------------ >> *From:* David Ham <David.Ham(a)imperial.ac.uk> >> *Sent:* 15 October 2015 12:07 >> *To:* William Booker; firedrake >> *Subject:* Re: Issues with Firedrake >> >> Dear William, >> >> Thanks for your email, I'm shifting this conversation onto the Firedrake >> mailing list, which is the appropriate place for Firedrake help requests. >> Please also see my responses below. >> >> On Thu, 15 Oct 2015 at 10:10 William Booker <scwb(a)leeds.ac.uk> wrote: >> >>> Dear David, >>> >>> I've been trying to get to grips with Firedrake by modifying the >>> advection demo. >>> >>> I'm trying to implement it as unsteady with a backwards euler timestep >>> but I've run into a few problems. >>> >>> First is that my initial condition does not appear to be implemented >>> correctly, as shown in the graph. It seems that instead of a shock, the IC >>> is smoothed out throughout the domain. >>> >> I've run your code, and the first thing to realise is that your first >> output is after the first timestep. The image you show is therefore after >> the tracer has begun to advect. This accounts for the "smearing out" and as >> far as I can see, the solution is entirely consistent with what you have >> specified. >> >> >>> >>> Second is that I'm not sure that my boundary conditions are actually >>> being set correctly, that is if I try to set the IC to be zero everywhere, >>> I'm not getting a value of 1 rising on the right side as I would expect. >>> >> >> I'm not sure why you expect this because the velocity field you have >> specified flows in the z direction, and the boundary condition is non-zero >> over the right half of the x-y (z=0) boundary. The advection equation >> therefore causes tracer to flux vertically through the right half of the >> domain until it is uniformly 1 and the left side is uniformly 0. This is >> what happens in the simulation, as far as I can see it's all correct. >> >> There is one small issue you may not have noticed, which is that the >> tracer is taking the value 0.5 when you might have expected 1.0. This is >> due to a subtle rounding error. When you project your tracer field, it is >> first being interpolated into DG1. In DG1, the top nodes of the bottom cell >> are (for rounding reasons) taking the value 0, which means the cell average >> value is 0.5. In this case, the simplest way around this is to interpolate >> the BC value straight into DG0. That is, replace: >> >> ic = project(inflow, V) >> >> with: >> >> ic = interpolate(inflow, V) >> >> >>> Finally I've tried to use a mesh made in gmsh but I've found if I don't >>> name the boundaries, I can't assign values using the 1,2,3,4 system. This >>> may be related to the previous point but if I try to assign names in gmsh, >>> Firedrake won't load the file with an error that it is not a valid gmsh >>> file. >>> >>> Firedrake is complaining that it's not a valid gmsh file because it >> isn't a valid gmsh file. If you check lines 8 and 9 of trapezium.msh you >> will see some junk which is directly quoted from the .geo file. There is >> clearly some issue with your .geo file. If I had to take a guess, I would >> say that there is a missing double quote character after Right. >> >> Regards, >> >> David >> >> >>> >>> Any help would be greatly appreciated, >>> >>> Will >>> >>

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Re: [firedrake] Issues with Firedrake
by David Ham 28 Oct '15

28 Oct '15

Aha. After a little experimentation, it turns out that PETSc does not support gmsh Physical Lines labelled with strings. If you replace the strings with (unique) numbers then it will work. This appears to be an upstream issue with PETSc. Regards, David On Thu, 22 Oct 2015 at 10:24 William Booker <scwb(a)leeds.ac.uk> wrote: > Dear Firedrakers, > > I fixed the physical name issue from last time but I'm still getting that > the msh file isn't valid. What can I do to correct this? > > Thanks in advance, > > Will > > > ------------------------------ > *From:* David Ham <David.Ham(a)imperial.ac.uk> > *Sent:* 15 October 2015 12:07 > *To:* William Booker; firedrake > *Subject:* Re: Issues with Firedrake > > Dear William, > > Thanks for your email, I'm shifting this conversation onto the Firedrake > mailing list, which is the appropriate place for Firedrake help requests. > Please also see my responses below. > > On Thu, 15 Oct 2015 at 10:10 William Booker <scwb(a)leeds.ac.uk> wrote: > >> Dear David, >> >> I've been trying to get to grips with Firedrake by modifying the >> advection demo. >> >> I'm trying to implement it as unsteady with a backwards euler timestep >> but I've run into a few problems. >> >> First is that my initial condition does not appear to be implemented >> correctly, as shown in the graph. It seems that instead of a shock, the IC >> is smoothed out throughout the domain. >> > I've run your code, and the first thing to realise is that your first > output is after the first timestep. The image you show is therefore after > the tracer has begun to advect. This accounts for the "smearing out" and as > far as I can see, the solution is entirely consistent with what you have > specified. > > >> >> Second is that I'm not sure that my boundary conditions are actually >> being set correctly, that is if I try to set the IC to be zero everywhere, >> I'm not getting a value of 1 rising on the right side as I would expect. >> > > I'm not sure why you expect this because the velocity field you have > specified flows in the z direction, and the boundary condition is non-zero > over the right half of the x-y (z=0) boundary. The advection equation > therefore causes tracer to flux vertically through the right half of the > domain until it is uniformly 1 and the left side is uniformly 0. This is > what happens in the simulation, as far as I can see it's all correct. > > There is one small issue you may not have noticed, which is that the > tracer is taking the value 0.5 when you might have expected 1.0. This is > due to a subtle rounding error. When you project your tracer field, it is > first being interpolated into DG1. In DG1, the top nodes of the bottom cell > are (for rounding reasons) taking the value 0, which means the cell average > value is 0.5. In this case, the simplest way around this is to interpolate > the BC value straight into DG0. That is, replace: > > ic = project(inflow, V) > > with: > > ic = interpolate(inflow, V) > > >> Finally I've tried to use a mesh made in gmsh but I've found if I don't >> name the boundaries, I can't assign values using the 1,2,3,4 system. This >> may be related to the previous point but if I try to assign names in gmsh, >> Firedrake won't load the file with an error that it is not a valid gmsh >> file. >> >> Firedrake is complaining that it's not a valid gmsh file because it isn't > a valid gmsh file. If you check lines 8 and 9 of trapezium.msh you will see > some junk which is directly quoted from the .geo file. There is clearly > some issue with your .geo file. If I had to take a guess, I would say that > there is a missing double quote character after Right. > > Regards, > > David > > >> >> Any help would be greatly appreciated, >> >> Will >> >

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UFL statement for python int()
by Buesing, Henrik 28 Oct '15

28 Oct '15

Dear all, I have a function temp(p,h), which returns temperature dependent on pressure and enthalpy. I insert UFL representations of p and h into temp(,). Then I do some +,-,*,/ operations and afterwards want something like python int(,). How do I do this in valid UFL syntax? And finally I want to access an array with the vector of values I got, and save the values I get back to the UFL form. Henrik -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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Modifying diagonal entries of Jacobian (preconditioning)
by Buesing, Henrik 27 Oct '15

27 Oct '15

Dear Firedrakers, if I wanted to modify the diagonal entries of my Jacobian in a Newton step during a time step... How would I do this? Do I have to define my own preconditioner here? Henrik -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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Re: [firedrake] WG: Dirichlet BC on extruded mesh with discontinuous function space
by David Ham 27 Oct '15

27 Oct '15

Hi Henrik, That is indeed the claim. Let us know if it works.... ;) David On Fri, 16 Oct 2015 at 12:09 Buesing, Henrik <HBuesing(a)eonerc.rwth-aachen.de> wrote: > Dear Firedrakers, > > > > Since https://github.com/firedrakeproject/firedrake/pull/600 has been > merged will > > > > *bc0 = DirichletBC(W.sub(0), Expression("1.0e7"), 2,method="geometric")* > > > > now work on a DG space on an extruded mesh (see below for actual code)? > > Do I just have to update firedrake for this to work? > > Thank you! > > Henrik > > > > > > > > -- > > Dipl.-Math. Henrik Büsing > > Institute for Applied Geophysics and Geothermal Energy > > E.ON Energy Research Center > > RWTH Aachen University > > ------------------------------------------------------ > > Mathieustr. 10 | Tel +49 (0)241 80 49907 > > 52074 Aachen, Germany | Fax +49 (0)241 80 49889 > > ------------------------------------------------------ > > http://www.eonerc.rwth-aachen.de/GGE > > hbuesing(a)eonerc.rwth-aachen.de > > ------------------------------------------------------ > > > > *Von:* firedrake-bounces(a)imperial.ac.uk [mailto: > firedrake-bounces(a)imperial.ac.uk] *Im Auftrag von *Buesing, Henrik > *Gesendet:* 23 September 2015 12:06 > *An:* firedrake(a)imperial.ac.uk > *Betreff:* [firedrake] Dirichlet BC on extruded mesh with discontinuous > function space > > > > Dear Firedrakers, > > > > I’m constructing a DG space on an extruded mesh. > > > > > > > > *meshbase = RectangleMesh(Nx, Ny, Lx, Ly, quadrilateral=True) mesh = > ExtrudedMesh(meshbase, Nz, Delta_z) horiz_elt = FiniteElement("DG", > quadrilateral, 0) vert_elt = FiniteElement("DG", interval, 0) elt = > OuterProductElement(horiz_elt, vert_elt)* > > *DG = FunctionSpace(mesh, elt)* > > *W=DG*DG* > > > > Now I would like to impose Dirchlet BC on one of the boundaries. > > I tried > > *bc0 = DirichletBC(W.sub(0), Expression("1.0e7"), 2,method="geometric")* > > > > and get a > > > > *ValueError: Geometric boundary conditions are not yet supported on > extruded meshes* > > > > Using the standard topological way, seems to have no effect at all. > > > > Is there a way around this? I would be fine with fixing the value on the > most outer cell layer, if that is possible… > > > > Henrik > > > > > > > > > > > > -- > > Dipl.-Math. Henrik Büsing > > Institute for Applied Geophysics and Geothermal Energy > > E.ON Energy Research Center > > RWTH Aachen University > > ------------------------------------------------------ > > Mathieustr. 10 | Tel +49 (0)241 80 49907 > > 52074 Aachen, Germany | Fax +49 (0)241 80 49889 > > ------------------------------------------------------ > > http://www.eonerc.rwth-aachen.de/GGE > > hbuesing(a)eonerc.rwth-aachen.de > > ------------------------------------------------------ > > >

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Re: [firedrake] firedrake-install error
by David Ham 23 Oct '15

23 Oct '15

Oh damn. I don't have one of those to test with. Hmm. Well I'll try a fresh install anyway to see if it breaks. On Fri, 23 Oct 2015 at 16:43 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > I am on Mavericks 10.9.5. > > > > On 23/10/15 16:39, David Ham wrote: > > Hmm. That's a new one. I can't say I immediately understand it, and my Mac > is at home today. I'll try to see if I can reproduce it tonight. Are you on > Yosemite? > > On Fri, 23 Oct 2015 at 15:20 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > >> That didn’t help but it seems that I homebrew was outdated, so I updated >> it and fixed all the warnings it caused. The firedrake installation then >> went a bit further, but still got the following error: >> >> Installing virtualenv. >> Downloading/unpacking virtualenv >> Downloading virtualenv-13.1.2-py2.py3-none-any.whl (1.7MB): 1.7MB >> downloaded >> Installing collected packages: virtualenv >> Cleaning up... >> Exception: >> Traceback (most recent call last): >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/basecommand.py", >> line 122, in main >> status = self.run(options, args) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/commands/install.py", >> line 283, in run >> requirement_set.install(install_options, global_options, >> root=options.root_path) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/req.py", >> line 1435, in install >> requirement.install(install_options, global_options, *args, **kwargs) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/req.py", >> line 671, in install >> self.move_wheel_files(self.source_dir, root=root) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/req.py", >> line 901, in move_wheel_files >> pycompile=self.pycompile, >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/wheel.py", >> line 141, in move_wheel_files >> scheme = distutils_scheme(name, user=user, home=home, root=root) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/locations.py", >> line 155, in distutils_scheme >> i.finalize_options() >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install.py", >> line 268, in finalize_options >> raise DistutilsOptionError("can't combine user with prefix, " >> DistutilsOptionError: can't combine user with prefix, exec_prefix/home, >> or install_(plat)base >> >> Storing debug log for failure in >> /var/folders/cs/cbmmbcd13mv9jq1cptvdljzsl5jfkj/T/tmpU1wo1M >> Traceback (most recent call last): >> File "firedrake-install", line 394, in <module> >> check_call(["pip", "install", "--user", "virtualenv"]) >> File "firedrake-install", line 163, in check_call >> subprocess.check_call(arguments) >> File >> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", >> line 540, in check_call >> raise CalledProcessError(retcode, cmd) >> subprocess.CalledProcessError: Command '['pip', 'install', '--user', >> 'virtualenv']' returned non-zero exit status 2 >> >> >> On 23 Oct 2015, at 14:04, Lawrence Mitchell < >> lawrence.mitchell(a)imperial.ac.uk> wrote: >> >> >> On 23 Oct 2015, at 13:27, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: >> >> Dear all, >> >> I tried to update firedrake on my Macbook using the firedrake-install >> script for the first time, but I got the error below. I can update >> successfully using the standard steps. >> >> Best, Anna. >> >> >> >> Hi Anna, >> >> Does everything work if you do: >> >> brew tap homebrew/science >> >> and then try firedrake-install again. >> >> Lawrence >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> >> > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- > > Dr Anna Kalogirou > Research Fellow > School of Mathematics > University of Leeds > > http://www1.maths.leeds.ac.uk/~matak/ > >

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