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Re: [firedrake] Mismatching function spaces error
by Andrew McRae 20 Mar '17

20 Mar '17

Good spot, this is the split(foo) vs foo.split() "gotcha". split(foo) is supposed to give symbolic UFL objects that can be used in forms: U = FunctionSpace(...); V = FunctionSpace(...) W = U*V urho = TrialFunction(W) u, rho = split(urho) # could have done u, rho = TrialFunctions(W) a = (u*.... + div(u)*.... + rho*...)*dx Whilst foo.split() splits a Function into subfunctions for further use (assignation, output, etc) urho_out = Function(W) solve(a == L, urho_out, bcs=...) u_out, rho_out = urho_out.split() File("temp.pvd").write(rho_out) Furthermore, these somehow work interchangeably *most of the time*, but not *all of the time*. Apologies. On 20 March 2017 at 07:48, Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > > Sorry, > Z0.assign(Z1_out) > ------------------------------ > *De :* Floriane Gidel [RPG] > *Envoyé :* lundi 20 mars 2017 07:47:28 > *À :* firedrake(a)imperial.ac.uk > *Objet :* RE: Mismatching function spaces error > > Hi Anna, > > I think you need to write something like > > Phi_out, eta_out, mu_out, Z1_out, W1_out, I_out = w.split() > Z0.assign(Z0_out) > > Best, > Floriane > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > *Envoyé :* dimanche 19 mars 2017 22:18:38 > *À :* firedrake(a)imperial.ac.uk > *Objet :* [firedrake] Mismatching function spaces error > > Dear all, > > I am defining a mixed system as follows: > > V = FunctionSpace(mesh, "CG", 1) > V_R = FunctionSpace(mesh, "R", 0) > W = V * V * V * V_R * V_R * V_R > > and some of the functions defined are: > > Z0 = Function(V_R) > w = Function(W) > phi, eta, mu, Z1, W1, I = split(w) > > After defining and solving some solvers etc, I do the following assignment > but run into a “Mismatching function spaces” error: > Z0.assign(Z1) > > Variable Z1 is solved in a mixed system and I want to assign it to Z0, > which belongs to space V_R. > Shouldn’t the assignment line above work? Why am I getting the error? > > Thank you, > > Anna. > > > On 19 Feb 2017, at 23:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > > Dear all, > > I am trying to solve a set of PDEs and ODEs together as a mixed system. > The ODE variables only depend on time, so I define them as functions from > the real function space R. > > First question: Is this a correct approach? > > Second question: I am running into a “Mismatching function spaces” error; > can someone please take a look at my code (found here > <https://bitbucket.org/annakalog/buoy2d/src/957e88739223e11d84826c76923a9b07…>) > and let me know what I’m doing wrong? The error arises when the value of > one of the mixed-system variables is assigned to another variable which > belongs to the same function space. [I remember having the same issue some > time ago, but I thought that it was fixed.] > > Thank you. > > Best, Anna. > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

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Re: [firedrake] circles in firedrake?
by Andrew McRae 20 Mar '17

20 Mar '17

As in, the gmsh input code that we used to create the circle mesh is being deleted in that commit, at lines 456-463. You could copy those removed lines into a .geo file and run it through gmsh to get the mesh that was being created before (but it has the cell area -> 0 problem). I would expect a user to run gmsh separately (at the command line or through the GUI), rather than from within the Python script. I don't think it's possible to interact with gmsh from Python nowadays without jumping through considerable hoops. Not sure why you're getting that error. It's been a long time since I last used gmsh. Taking a guess from https://github.com/FluidityProject/fluidity/wiki/Gmsh-tutorial, try adding one more line to the .geo: Physical Surface(7) = {6}; On 19 March 2017 at 16:04, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Thank you Andrew for your help. I am a bit sorry to see CircleMesh go > away but if it only gave a structured mesh, then I can see the advantage to > using gmsh. Also, I should really learn how to use gmsh better, so this > will force me to do just that. > > I looked around for circle.geo but couldn't find it in the repo. > > I found another version of circle.geo that seems to build a circle. It is > copied here > > L = 10; > dx = 1; > > Point(1) = { 0, 0, 0, dx}; > Point(2) = { L, 0, 0, dx}; > Point(3) = {-L, 0, 0, dx}; > Point(4) = { 0, L, 0, dx}; > Point(5) = { 0,-L, 0, dx}; > > Circle(1) = {3,1,5}; > Circle(2) = {5,1,2}; > Circle(3) = {2,1,4}; > Circle(4) = {4,1,3}; > > Line Loop(5) = {1,2,3,4}; > > Plane Surface(6) = {5}; > > I am not sure why the origin needs to be included but it does give the > correct shape at least. > > Unfortunately, when I try importing this in firedrake using > > from firedrake import * > > #gmsh -2 circle.geo > > mesh = Mesh("circle.msh") > > > I get the error > > Traceback (most recent call last): > File "test.py", line 7, in <module> > mesh = Mesh("circle.msh") > File "<decorator-gen-261>", line 2, in Mesh > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/profiling.py", > line 61, in wrapper > return f(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/mesh.py", > line 1259, in Mesh > topology = MeshTopology(plex, name=name, reorder=reorder, > distribute=distribute) > File "<decorator-gen-259>", line 2, in __init__ > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/profiling.py", > line 61, in wrapper > return f(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/mesh.py", > line 348, in __init__ > dmplex.validate_mesh(plex) > File "firedrake/dmplex.pyx", line 1009, in > firedrake.dmplex.validate_mesh (firedrake/dmplex.c:14063) > ValueError: Provided mesh has some entities not reachable by traversing > cells (maybe rogue vertices?) > > > Can you point out what I'm doing wrong? Or where to find the circle.geo? > > Also, I tried use gmsh in firedrake as commented above and that didn't > work. Should gmsh work in the latest version? > > 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 Andrew McRae [A.T.T.McRae(a)bath.ac.uk] > *Sent:* Sunday, March 19, 2017 8:07 AM > *To:* firedrake(a)imperial.ac.uk > *Subject:* Re: [firedrake] circles in firedrake? > > We used to have a CircleMesh in Firedrake, but it was removed in this > commit > <https://github.com/firedrakeproject/firedrake/commit/54bff6b70e046106ddd4e7…>. > If I recall correctly, this is because we outsourced the creation of that > mesh to gmsh, but the gmsh-from-Python packages are no longer available > with newer versions of Ubuntu. > > That commit has a small gmsh snippet (.geo). You could manually run this > through gmsh to build a mesh (.msh), and load this in to your firedrake > script: mesh = Mesh("circle.msh"). Note that this CircleMesh (and, IIRC, > FEniCS's equivalent) give a "structured" mesh with radial lines, and > correspondingly small cells in the middle. If this is undesirable, you > might be better off making a simple unstructured circle mesh in gmsh and > loading it in. > > Regarding the code you gave in your email, I think this has also worked > just fine. However, the built-in Firedrake plotting functionality only > seems to support 2D triangle and "unstructured" quadrilateral cells, rather > than the "interval x interval" cells created by an extruded mesh. (I > suspect this was an accidental omission) > > If you instead do File("temp.pvd").write(U) and open the result in > Paraview, I'm sure it would look fine. Of course, if you use this to get a > circular mesh, it will also have small cells at the centre. > > Best, > Andrew > > On 18 March 2017 at 17:29, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > >> Hello, >> >> I want to define my mesh to be a circle. In Fenics I know there is a >> command called CircleMesh that makes this very easy. >> >> Q1) Is there a simple way of doing this in Firedrake? >> >> I looked around and see how circlemanifoldmesh can do this with help for >> ExtrudedMesh. I found some code that can make a ring and I tried running >> it myself and defining a function on that mesh. Unfortunately, I get an >> error, see below. >> >> Q2) If one needs to use CircleManifoldMesh is there something else one >> needs to do to use a circular geometry as your mesh? >> >> Below are the lines that I tried and the error >> >>> from firedrake import * >> >>> m = CircleManifoldMesh(20, radius=2) >> >>> mesh = ExtrudedMesh(m, 5, extrusion_type='radial') >> >>> x = SpatialCoordinate(mesh) >> >>> V = FunctionSpace(mesh,'CG',1) >> >>> U = Function(V).interpolate(-(pow(x[0]-0.5,2) + pow(x[1]-0.5,2))) >> >>> plot(U); >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 308, in plot >> **kwargs) >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 502, in two_dimension_plot >> num_sample_points) >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 457, in _two_dimension_triangle_func_val >> raise RuntimeError("Unsupported Functionality") >> RuntimeError: Unsupported Functionality >> >> >> ------------------ >> 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> >> >> >

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Re: [firedrake] circles in firedrake?
by Andrew McRae 19 Mar '17

19 Mar '17

Good to hear. I'm slightly surprised that snippet works: gmsh documentation says that Circle creates an arc of angle "(strictly) smaller than Pi", which is why the usual snippet breaks it into 4 quarter-circle segments (slightly cleaner than 3, I guess). On 19 March 2017 at 16:31, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Thank you Andrew. > > Adding a Physical Surface was what I was missing. > > I found a more compact version and including it here, in case others might > benefit from it. > > // mesh width associated with points > lc = 0.1; > ln = 1.0; > > // Two antipodal points on the circle, the third point is the circle center > Point(1) = {-ln, 0, 0, lc}; > Point(2) = { ln, 0, 0, lc}; > Point(3) = { 0, 0, 0, lc}; > > Circle(1) = {1,3,2}; > Circle(2) = {2,3,1}; > > Line Loop(100) = {1,2}; > > Plane Surface(200) = {100}; > > Physical Surface(300) = {200}; > > > Also, I now see that it's silly to wan to run gmsh on firedrake. Sorry. > > 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 Francis Poulin [fpoulin(a)uwaterloo.ca] > *Sent:* Sunday, March 19, 2017 12:04 PM > *To:* firedrake(a)imperial.ac.uk > *Subject:* Re: [firedrake] circles in firedrake? > > Thank you Andrew for your help. I am a bit sorry to see CircleMesh go > away but if it only gave a structured mesh, then I can see the advantage to > using gmsh. Also, I should really learn how to use gmsh better, so this > will force me to do just that. > > I looked around for circle.geo but couldn't find it in the repo. > > I found another version of circle.geo that seems to build a circle. It is > copied here > > L = 10; > dx = 1; > > Point(1) = { 0, 0, 0, dx}; > Point(2) = { L, 0, 0, dx}; > Point(3) = {-L, 0, 0, dx}; > Point(4) = { 0, L, 0, dx}; > Point(5) = { 0,-L, 0, dx}; > > Circle(1) = {3,1,5}; > Circle(2) = {5,1,2}; > Circle(3) = {2,1,4}; > Circle(4) = {4,1,3}; > > Line Loop(5) = {1,2,3,4}; > > Plane Surface(6) = {5}; > > I am not sure why the origin needs to be included but it does give the > correct shape at least. > > Unfortunately, when I try importing this in firedrake using > > from firedrake import * > > #gmsh -2 circle.geo > > mesh = Mesh("circle.msh") > > > I get the error > > Traceback (most recent call last): > File "test.py", line 7, in <module> > mesh = Mesh("circle.msh") > File "<decorator-gen-261>", line 2, in Mesh > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/profiling.py", > line 61, in wrapper > return f(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/mesh.py", > line 1259, in Mesh > topology = MeshTopology(plex, name=name, reorder=reorder, > distribute=distribute) > File "<decorator-gen-259>", line 2, in __init__ > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/profiling.py", > line 61, in wrapper > return f(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/mesh.py", > line 348, in __init__ > dmplex.validate_mesh(plex) > File "firedrake/dmplex.pyx", line 1009, in > firedrake.dmplex.validate_mesh (firedrake/dmplex.c:14063) > ValueError: Provided mesh has some entities not reachable by traversing > cells (maybe rogue vertices?) > > > Can you point out what I'm doing wrong? Or where to find the circle.geo? > > Also, I tried use gmsh in firedrake as commented above and that didn't > work. Should gmsh work in the latest version? > > 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 Andrew McRae [A.T.T.McRae(a)bath.ac.uk] > *Sent:* Sunday, March 19, 2017 8:07 AM > *To:* firedrake(a)imperial.ac.uk > *Subject:* Re: [firedrake] circles in firedrake? > > We used to have a CircleMesh in Firedrake, but it was removed in this > commit > <https://github.com/firedrakeproject/firedrake/commit/54bff6b70e046106ddd4e7…>. > If I recall correctly, this is because we outsourced the creation of that > mesh to gmsh, but the gmsh-from-Python packages are no longer available > with newer versions of Ubuntu. > > That commit has a small gmsh snippet (.geo). You could manually run this > through gmsh to build a mesh (.msh), and load this in to your firedrake > script: mesh = Mesh("circle.msh"). Note that this CircleMesh (and, IIRC, > FEniCS's equivalent) give a "structured" mesh with radial lines, and > correspondingly small cells in the middle. If this is undesirable, you > might be better off making a simple unstructured circle mesh in gmsh and > loading it in. > > Regarding the code you gave in your email, I think this has also worked > just fine. However, the built-in Firedrake plotting functionality only > seems to support 2D triangle and "unstructured" quadrilateral cells, rather > than the "interval x interval" cells created by an extruded mesh. (I > suspect this was an accidental omission) > > If you instead do File("temp.pvd").write(U) and open the result in > Paraview, I'm sure it would look fine. Of course, if you use this to get a > circular mesh, it will also have small cells at the centre. > > Best, > Andrew > > On 18 March 2017 at 17:29, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > >> Hello, >> >> I want to define my mesh to be a circle. In Fenics I know there is a >> command called CircleMesh that makes this very easy. >> >> Q1) Is there a simple way of doing this in Firedrake? >> >> I looked around and see how circlemanifoldmesh can do this with help for >> ExtrudedMesh. I found some code that can make a ring and I tried running >> it myself and defining a function on that mesh. Unfortunately, I get an >> error, see below. >> >> Q2) If one needs to use CircleManifoldMesh is there something else one >> needs to do to use a circular geometry as your mesh? >> >> Below are the lines that I tried and the error >> >>> from firedrake import * >> >>> m = CircleManifoldMesh(20, radius=2) >> >>> mesh = ExtrudedMesh(m, 5, extrusion_type='radial') >> >>> x = SpatialCoordinate(mesh) >> >>> V = FunctionSpace(mesh,'CG',1) >> >>> U = Function(V).interpolate(-(pow(x[0]-0.5,2) + pow(x[1]-0.5,2))) >> >>> plot(U); >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 308, in plot >> **kwargs) >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 502, in two_dimension_plot >> num_sample_points) >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", >> line 457, in _two_dimension_triangle_func_val >> raise RuntimeError("Unsupported Functionality") >> RuntimeError: Unsupported Functionality >> >> >> ------------------ >> 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> >> >> >

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Re: [firedrake] circles in firedrake?
by Andrew McRae 19 Mar '17

19 Mar '17

We used to have a CircleMesh in Firedrake, but it was removed in this commit <https://github.com/firedrakeproject/firedrake/commit/54bff6b70e046106ddd4e7…>. If I recall correctly, this is because we outsourced the creation of that mesh to gmsh, but the gmsh-from-Python packages are no longer available with newer versions of Ubuntu. That commit has a small gmsh snippet (.geo). You could manually run this through gmsh to build a mesh (.msh), and load this in to your firedrake script: mesh = Mesh("circle.msh"). Note that this CircleMesh (and, IIRC, FEniCS's equivalent) give a "structured" mesh with radial lines, and correspondingly small cells in the middle. If this is undesirable, you might be better off making a simple unstructured circle mesh in gmsh and loading it in. Regarding the code you gave in your email, I think this has also worked just fine. However, the built-in Firedrake plotting functionality only seems to support 2D triangle and "unstructured" quadrilateral cells, rather than the "interval x interval" cells created by an extruded mesh. (I suspect this was an accidental omission) If you instead do File("temp.pvd").write(U) and open the result in Paraview, I'm sure it would look fine. Of course, if you use this to get a circular mesh, it will also have small cells at the centre. Best, Andrew On 18 March 2017 at 17:29, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > I want to define my mesh to be a circle. In Fenics I know there is a > command called CircleMesh that makes this very easy. > > Q1) Is there a simple way of doing this in Firedrake? > > I looked around and see how circlemanifoldmesh can do this with help for > ExtrudedMesh. I found some code that can make a ring and I tried running > it myself and defining a function on that mesh. Unfortunately, I get an > error, see below. > > Q2) If one needs to use CircleManifoldMesh is there something else one > needs to do to use a circular geometry as your mesh? > > Below are the lines that I tried and the error > >>> from firedrake import * > >>> m = CircleManifoldMesh(20, radius=2) > >>> mesh = ExtrudedMesh(m, 5, extrusion_type='radial') > >>> x = SpatialCoordinate(mesh) > >>> V = FunctionSpace(mesh,'CG',1) > >>> U = Function(V).interpolate(-(pow(x[0]-0.5,2) + pow(x[1]-0.5,2))) > >>> plot(U); > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", > line 308, in plot > **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", > line 502, in two_dimension_plot > num_sample_points) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", > line 457, in _two_dimension_triangle_func_val > raise RuntimeError("Unsupported Functionality") > RuntimeError: Unsupported Functionality > > > ------------------ > 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> > >

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Re: [firedrake] Changing a vector valued function in time loop
by David Ham 19 Mar '17

19 Mar '17

Also please note that c string functions are error-prone and deprecated. Please interpolate ufl expressions instead. Regards, David On Sun, 19 Mar 2017 at 13:48 William Booker <scwb(a)leeds.ac.uk> wrote: > Yep that was it. > > I feel silly now. > > Thanks > > Will > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > on behalf of Andrew McRae <A.T.T.McRae(a)bath.ac.uk> > *Sent:* 19 March 2017 13:40:42 > *To:* firedrake(a)imperial.ac.uk > *Subject:* Re: [firedrake] Changing a vector valued function in time loop > > -- I suspect you used the label 'a' to define a Function, but then reused > it to define your bilinear form. This would explain the error you allude > to. > > On 19 March 2017 at 13:36, Andrew McRae <A.T.T.McRae(a)bath.ac.uk> wrote: > > I'm not sure what error you're seeing (it would help if you'd posted a > full stack trace). > > However, I think the normal way to do this is to declare the expression > separately: > > a_expr = Expression(["0.5*F0*cos(omega*t)*x[1]", > "-0.5*F0*cos(omega*t)*x[0]"], F0=F0, omega=omega, t=t) > a.interpolate(a_expr) > > Inside the time loop, you then update any quantities that you need, and > reinterpolate: > > a_expr.t = t (or maybe a_expr.t.assign(t), I've forgotten...) > a.interpolate(a_expr) > > This is better than creating a new Expression object each time you go > around the loop, which is what it looks like you are doing at the moment. > > On 19 March 2017 at 13:27, William Booker <scwb(a)leeds.ac.uk> wrote: > > Dear Firedrakers, > > I'm trying to update a vector function in my time loop > > a.interpolate(Expression(["0.5*F0*cos(omega*t)*x[1]", > "-0.5*F0*cos(omega*t)*x[0]"], F0=F0, omega=omega, t=t)) > > but if I use assign or interpolate, I get told the form does not have the > respective property. > How should I go about making this work, such that it'll change the value > of a in my solver? > > Thanks > > will > > > > -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Changing a vector valued function in time loop
by Andrew McRae 19 Mar '17

19 Mar '17

I'm not sure what error you're seeing (it would help if you'd posted a full stack trace). However, I think the normal way to do this is to declare the expression separately: a_expr = Expression(["0.5*F0*cos(omega*t)*x[1]", "-0.5*F0*cos(omega*t)*x[0]"], F0=F0, omega=omega, t=t) a.interpolate(a_expr) Inside the time loop, you then update any quantities that you need, and reinterpolate: a_expr.t = t (or maybe a_expr.t.assign(t), I've forgotten...) a.interpolate(a_expr) This is better than creating a new Expression object each time you go around the loop, which is what it looks like you are doing at the moment. On 19 March 2017 at 13:27, William Booker <scwb(a)leeds.ac.uk> wrote: > Dear Firedrakers, > > I'm trying to update a vector function in my time loop > > a.interpolate(Expression(["0.5*F0*cos(omega*t)*x[1]", > "-0.5*F0*cos(omega*t)*x[0]"], F0=F0, omega=omega, t=t)) > > but if I use assign or interpolate, I get told the form does not have the > respective property. > How should I go about making this work, such that it'll change the value > of a in my solver? > > Thanks > > will >

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Changing a vector valued function in time loop
by William Booker 19 Mar '17

19 Mar '17

Dear Firedrakers, I'm trying to update a vector function in my time loop a.interpolate(Expression(["0.5*F0*cos(omega*t)*x[1]", "-0.5*F0*cos(omega*t)*x[0]"], F0=F0, omega=omega, t=t)) but if I use assign or interpolate, I get told the form does not have the respective property. How should I go about making this work, such that it'll change the value of a in my solver? Thanks will

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Re: [firedrake] Solver error
by Andrew McRae 19 Mar '17

19 Mar '17

The error is "Adding expressions with non-matching form arguments" Most likely you have a typo in one of the symbolic expressions. As a result, you are adding a form containing just a test function to one containing just a trial function, or something similar. Best, Andrew On 19 March 2017 at 11:37, William Booker <scwb(a)leeds.ac.uk> wrote: > Hi, > > How do I fix the following error for the solver? > > File "2d_compressible_stratified.py", line 195, in <module> > solver = LinearVariationalSolver(problem, > solver_parameters={'ksp_rtol': 1e-14}) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/variational_solver.py", line 286, in __init__ > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/variational_solver.py", line 156, in __init__ > pre_function_callback=pre_f_callback) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/solving_utils.py", line 226, in __init__ > appctx=appctx) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/assemble.py", line 120, in allocate_matrix > allocate_only=True) > File "<decorator-gen-279>", line 2, in _assemble > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/utils.py", > line 62, in wrapper > return f(*args, **kwargs) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/assemble.py", line 192, in _assemble > kernels = tsfc_interface.compile_form(f, "form", > parameters=form_compiler_parameters, inverse=inverse) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/tsfc_interface.py", line 193, in compile_form > number_map).kernels > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/PyOP2/pyop2/caching.py", > line 200, in __new__ > obj = make_obj() > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/PyOP2/pyop2/caching.py", > line 190, in make_obj > obj.__init__(*args, **kwargs) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ > firedrake/firedrake/tsfc_interface.py", line 112, in __init__ > tree = tsfc_compile_form(form, prefix=name, parameters=parameters) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/tsfc/tsfc/driver.py", > line 44, in compile_form > fd = ufl_utils.compute_form_data(form) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/tsfc/tsfc/ufl_utils.py", > line 56, in compute_form_data > do_estimate_degrees=do_estimate_degrees, > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ > ufl/algorithms/compute_form_data.py", line 387, in compute_form_data > check_form_arity(preprocessed_form, self.original_form.arguments()) > # Currently testing how fast this is > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ > ufl/algorithms/check_arities.py", line 152, in check_form_arity > check_integrand_arity(itg.integrand(), arguments) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ > ufl/algorithms/check_arities.py", line 145, in check_integrand_arity > args = map_expr_dag(rules, expr, compress=False) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/corealg/map_dag.py", > line 37, in map_expr_dag > result, = map_expr_dags(function, [expression], compress=compress) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/corealg/map_dag.py", > line 86, in map_expr_dags > r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands]) > File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ > ufl/algorithms/check_arities.py", line 42, in sum > raise ArityMismatch("Adding expressions with non-matching form > arguments {0} vs {1}.".format(a, b)) > ufl.algorithms.check_arities.ArityMismatch: Adding expressions with > non-matching form arguments (Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, > VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), > dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > triangle, 1), dim=2), 1)), 0, None), Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, > VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), > dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > triangle, 1), dim=2), 1)), 1, None)) vs (Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, > VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), > dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > triangle, 1), dim=2), 1)), 0, None),). > > >

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Solver error
by William Booker 19 Mar '17

19 Mar '17

Hi, How do I fix the following error for the solver? File "2d_compressible_stratified.py", line 195, in <module> solver = LinearVariationalSolver(problem, solver_parameters={'ksp_rtol': 1e-14}) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/variational_solver.py", line 286, in __init__ super(LinearVariationalSolver, self).__init__(*args, **kwargs) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/variational_solver.py", line 156, in __init__ pre_function_callback=pre_f_callback) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/solving_utils.py", line 226, in __init__ appctx=appctx) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/assemble.py", line 120, in allocate_matrix allocate_only=True) File "<decorator-gen-279>", line 2, in _assemble File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/assemble.py", line 192, in _assemble kernels = tsfc_interface.compile_form(f, "form", parameters=form_compiler_parameters, inverse=inverse) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 193, in compile_form number_map).kernels File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/PyOP2/pyop2/caching.py", line 200, in __new__ obj = make_obj() File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/PyOP2/pyop2/caching.py", line 190, in make_obj obj.__init__(*args, **kwargs) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 112, in __init__ tree = tsfc_compile_form(form, prefix=name, parameters=parameters) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/tsfc/tsfc/driver.py", line 44, in compile_form fd = ufl_utils.compute_form_data(form) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/tsfc/tsfc/ufl_utils.py", line 56, in compute_form_data do_estimate_degrees=do_estimate_degrees, File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/algorithms/compute_form_data.py", line 387, in compute_form_data check_form_arity(preprocessed_form, self.original_form.arguments()) # Currently testing how fast this is File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 152, in check_form_arity check_integrand_arity(itg.integrand(), arguments) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 145, in check_integrand_arity args = map_expr_dag(rules, expr, compress=False) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/corealg/map_dag.py", line 37, in map_expr_dag result, = map_expr_dags(function, [expression], compress=compress) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/corealg/map_dag.py", line 86, in map_expr_dags r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands]) File "/usr/not-backed-up/firedrake/2017-02-28/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 42, in sum raise ArityMismatch("Adding expressions with non-matching form arguments {0} vs {1}.".format(a, b)) ufl.algorithms.check_arities.ArityMismatch: Adding expressions with non-matching form arguments (Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 1)), 0, None), Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 1)), 1, None)) vs (Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f105c981410>, VectorElement(FiniteElement('Discontinuous Lagrange', triangle, 2), dim=2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 1)), 0, None),).

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circles in firedrake?
by Francis Poulin 18 Mar '17

18 Mar '17

Hello, I want to define my mesh to be a circle. In Fenics I know there is a command called CircleMesh that makes this very easy. Q1) Is there a simple way of doing this in Firedrake? I looked around and see how circlemanifoldmesh can do this with help for ExtrudedMesh. I found some code that can make a ring and I tried running it myself and defining a function on that mesh. Unfortunately, I get an error, see below. Q2) If one needs to use CircleManifoldMesh is there something else one needs to do to use a circular geometry as your mesh? Below are the lines that I tried and the error >>> from firedrake import * >>> m = CircleManifoldMesh(20, radius=2) >>> mesh = ExtrudedMesh(m, 5, extrusion_type='radial') >>> x = SpatialCoordinate(mesh) >>> V = FunctionSpace(mesh,'CG',1) >>> U = Function(V).interpolate(-(pow(x[0]-0.5,2) + pow(x[1]-0.5,2))) >>> plot(U); Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", line 308, in plot **kwargs) File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", line 502, in two_dimension_plot num_sample_points) File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.py", line 457, in _two_dimension_triangle_func_val raise RuntimeError("Unsupported Functionality") RuntimeError: Unsupported Functionality ------------------ 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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