December 2015 - firedrake - imperial.ac.uk

assembly_cache error
by Anna Kalogirou 11 Dec '15

11 Dec '15

Dear all, I get an error similar to an old error reported here: https://github.com/firedrakeproject/firedrake/issues/303 The error is fixed when adding David's suggestion " parameters["assembly_cache"]["enabled"] = False " at the top of the script, but it seems weird because I am not running in parallel. I am attaching two files if you want to see the lines where the error appears. The traceback of the error is the following: -------------------------------------------------------- File "buoy-swe.py", line 131, in <module> (phi0, eta0, W0, Z0) = solvers_SV(rhs, mu0_5, mu_solver0_5, phi_solver0_5, eta_solver1, phi_solver1, eta0, phi0, Z0, W0, eta1, phi1, Z1, W1, W0_5, step_b, rho, Mass, dt); File "/e/data1/users/matak/opt/firedrake/Ship/Modules/Wave-maker/solvers.py", line 164, in solvers_SV phi_solver0_5.solve() # Solve for phi0_5 File "<string>", line 2, in solve File "/opt/firedrake/3.0/lib/python2.7/site-packages/PyOP2-0.11.0_173_g1e3c1eb-py2.7-linux-x86_64.egg/pyop2/profiling.py", line 197, in wrapper return f(*args, **kwargs) File "/opt/firedrake/3.0/lib/python2.7/site-packages/firedrake/variational_solver.py", line 287, in solve self.snes.solve(None, v) File "PETSc/SNES.pyx", line 516, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:161228) File "PETSc/petscsnes.pxi", line 284, in petsc4py.PETSc.SNES_Jacobian (src/petsc4py.PETSc.c:31311) File "/opt/firedrake/3.0/lib/python2.7/site-packages/firedrake/variational_solver.py", line 175, in form_jacobian ctx._jac.M._force_evaluation() File "/opt/firedrake/3.0/lib/python2.7/site-packages/firedrake/matrix.py", line 143, in M self.assemble() File "/opt/firedrake/3.0/lib/python2.7/site-packages/firedrake/matrix.py", line 72, in assemble self._assembly_callback(self.bcs) File "/opt/firedrake/3.0/lib/python2.7/site-packages/firedrake/assembly_cache.py", line 340, in inner PETSc.Mat.Structure.DIFFERENT_NONZERO_PATTERN) File "PETSc/Mat.pyx", line 616, in petsc4py.PETSc.Mat.copy (src/petsc4py.PETSc.c:113902) petsc4py.PETSc.Error: error code 73 [0] SNESSolve() line 3840 in /tmp/pip-0XEmR8-build/src/snes/interface/snes.c [0] SNESSolve_KSPONLY() line 41 in /tmp/pip-0XEmR8-build/src/snes/impls/ksponly/ksponly.c [0] SNESComputeJacobian() line 2203 in /tmp/pip-0XEmR8-build/src/snes/interface/snes.c [0] MatCopy() line 3771 in /tmp/pip-0XEmR8-build/src/mat/interface/matrix.c [0] Object is in wrong state [0] Not for factored matrix Thanks, Anna.

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Problems with assembly and expressions
by William Booker 11 Dec '15

11 Dec '15

Dear all, I've been trying to assemble my initial energy to check my initial conditions, E = \int \frac{1}{2 \rho_0}(\rho_0 \underline{u}^2) + \frac{g^2}{2 \rho_0 N^2} ( \rho - \frac{p}{c^2_0} ) ^2 + \frac{ p^2}{2 \rho_0 c^2_0} dx #Initial Energy E_0 = assemble( (0.5*inner((u_),(u_))/r_0 + 0.5*pow(g,2)*( r_ - p_/c_0)**2/(r_0*N) + 0.5* p_**2/(r_0*c_0))*dx ) but I get the following error message pyop2:INFO Compiling wrapper... Traceback (most recent call last): File "compressible.py", line 87, in <module> E_0 = assemble( (0.5*inner((u_),(u_))/r_0 + 0.5*pow(g,2)*( r_ - p_/c_0)**2/(r_0*N) + 0.5* p_**2/(r_0*c_0))*dx ) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 68, in assemble inverse=inverse, nest=nest) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 450, in _assemble return thunk(bcs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assembly_cache.py", line 350, in inner r = thunk(bcs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 442, in thunk return result() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 219, in <lambda> result = lambda: tensor.data[0] pyop2:INFO Compiling wrapper... Traceback (most recent call last): File "compressible.py", line 87, in <module> E_0 = assemble( (0.5*inner((u_),(u_))/r_0 + 0.5*pow(g,2)*( r_ - p_/c_0)**2/(r_0*N) + 0.5* p_**2/(r_0*c_0))*dx ) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 68, in assemble inverse=inverse, nest=nest) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 450, in _assemble return thunk(bcs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assembly_cache.py", line 350, in inner r = thunk(bcs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 442, in thunk return result() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 219, in <lambda> result = lambda: tensor.data[0] File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 2741, in data _trace.evaluate(set([self]), set()) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 169, in evaluate comp._run() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 4032, in _run return self.compute() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 4073, in compute fun = self._jitmodule File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/sequential.py", line 147, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/host.py", line 687, in __init__ self.compile() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/host.py", line 785, in compile compiler=compiler.get('name')) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/compilation.py", line 270, in load dll = compiler.get_so(src, extension) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/compilation.py", line 139, in get_so Original error: %s""" % (cc, logfile, errfile, e)) pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-g', '-O3', '-fno-tree-vectorize', '-I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/include', '-I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2', '-msse', '-o', '/tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.so.tmp', '/tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.c', '-shared', '-L/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib', '-Wl,-rpath,/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib', '-lpetsc', '-lm']" returned with error. Unable to compile code Compile log in /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.log Compile errors in /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.err Original error: status 1 invoking 'mpicc -std=c99 -fPIC -Wall -g -O3 -fno-tree-vectorize -I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/include -I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2 -msse -o /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.so.tmp /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.c -shared -L/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib -lpetsc -lm' File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 2741, in data _trace.evaluate(set([self]), set()) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 169, in evaluate comp._run() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 4032, in _run return self.compute() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/base.py", line 4073, in compute fun = self._jitmodule File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/sequential.py", line 147, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/host.py", line 687, in __init__ self.compile() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/host.py", line 785, in compile compiler=compiler.get('name')) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/compilation.py", line 270, in load dll = compiler.get_so(src, extension) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/compilation.py", line 139, in get_so Original error: %s""" % (cc, logfile, errfile, e)) pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-g', '-O3', '-fno-tree-vectorize', '-I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/include', '-I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2', '-msse', '-o', '/tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.so.tmp', '/tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.c', '-shared', '-L/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib', '-Wl,-rpath,/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib', '-lpetsc', '-lm']" returned with error. Unable to compile code Compile log in /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.log Compile errors in /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.err Original error: status 1 invoking 'mpicc -std=c99 -fPIC -Wall -g -O3 -fno-tree-vectorize -I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/include -I/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2 -msse -o /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.so.tmp /tmp/pyop2-cache-uid368130/13e27493d91e2c8a482fd450a665bf54_p10909.c -shared -L/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/petsc/lib -lpetsc -lm' Would this be because my expression and bcs don't match bc I haven't tried that yet, as the current bcs are only placeholders for real expressions later on. thanks Will

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Paraview
by Anna Kalogirou 11 Dec '15

11 Dec '15

Dear all, I have a question which is related to visualising results with Paraview, so I thought maybe someone here can help. I would like to plot the coordinates (x,y) of specific point (similar to the red circle in the picture attached) on the same plot as the solution. These coordinates change at every time step and I can calculate them as save them in a .csv file, which I can load to Paraview. However, I don't know which filters I need to apply in order to create the desired outcome. Any ideas would be appreciated. Thanks! Best, Anna.

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2D to 3D function
by Floriane Gidel [RPG] 10 Dec '15

10 Dec '15

Dear all, First of all, thanks a lot for your time last Friday, and your help both for the implementation and for the installation of Firedrake. I am now trying to implement the equations we discussed on Friday, for the 3D potential flow equations. As a reminder, I solve the equations for phi, h, but also phi_s which is a 3D function, but is only updated at the free surface. However, I would like to update the interior nodes of phi_s as well, by copying the value of its surface nodes, as soon as they are updated (that is, simultaneously with solving the coupled equations). Is there a way to do this? I attach a short pdf summarising the equations, the current implementation and the issue I get. Thank you very much, Floriane

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Initial conditions in a mixed function space
by William Booker 10 Dec '15

10 Dec '15

Dear all, I hope I have not missed something obvious again but I'm looking to assign initial conditions for my variables \underline{u} , \rho and p. Velocity, density and pressure respectively. I have a mixed function space W, and my first thought was to define initial variables by splitting a W function w_ = Function(W) (u_, r_, p_) = split(w_) and then interpolating my expression for the exact solution for each variable u_.sub(0).interpolate(exact_w) r_.interpolate(exact_r) but as I get the error File "compressible.py", line 74, in <module> r_.interpolate(exact_r) AttributeError: 'Indexed' object has no attribute 'interpolate' this is clearly not the way to go. What would be a better approach ? Will

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Re: [firedrake] Tetrahedral mesh
by David Ham 10 Dec '15

10 Dec '15

Dear David, I think you have confused what Lawrence was asking. Since you are working with Sebastian Reich, we assume you are solving atmospheric problems. In this context, the definite Helmholtz equation usually occurs: laplacian u - u = f while you appear to be solving the indefinite Helmholtz equation: laplacian u + u = f We were just attempting to ascertain whether you were deliberately solving the indefinite version of the problem. Is this the case? David On Thu, 10 Dec 2015 at 14:47 Angwenyi David <kipkoej(a)gmail.com> wrote: > Integration by parts is equivalent to using Green’s function; and so it > turns out as follows: > > laplacian u = - u + f > Greens function: integ((laplacian u)v) + integ(dot(grad u, grad v)) = > surfinteg((partial_n u)v) > > So that the weak form is obtained by substituting laplacian u = -u + f > from the Helmholtz equation in the Green’s function. The same is arrived at > by integration by parts. > > Sincerely, > > David > > > On 10 Dec 2015, at 15:23, Lawrence Mitchell < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > > > > > On 10/12/15 14:12, Angwenyi David wrote: > >>>>> nx = 10 > >>>>> ny = 10 > >>>>> nz = 20 > >>>>> mesh = BoxMesh(nx, ny, nz, 1.0, 1.0, 2.0) > >>>>> V = FunctionSpace(mesh, "CG", 1) > >>>>> u = TrialFunction(V) > >>>>> v = TestFunction(V) > >>>>> f = Function(V) > >>>>> f.interpolate(Expression("(2*x[0])+(3*x[1])+(0.5*x[2])")) > >> Coefficient(FunctionSpace(Mesh(VectorElement('Lagrange', tetrahedron, > >> 1, dim=3), 3), FiniteElement('Lagrange', tetrahedron, 1)), 4) > >>>>> a = (dot(grad(v), grad(u)) - v * u) * dx > > > > This is the indefinite form of the Helmholtz equation. Did you > > actually want the sign-positive Helmholtz equation? > > > > The later has strong form: > > > > -laplacian u + u = f > > > > When integrating by parts the weak form becomes: > > > > <grad u, grad v> + <u, v> = <f, v> > > > > As to incorporation of boundary conditions, see > > > > > http://firedrakeproject.org/variational-problems.html#incorporating-boundar… > > > > Cheers, > > > > Lawrence > > > > _______________________________________________ > > 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 >

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Re: [firedrake] Tetrahedral mesh
by Andrew McRae 10 Dec '15

10 Dec '15

This is after doing mesh = BoxMesh (...) On 9 Dec 2015 15:19, "Angwenyi David" <kipkoej(a)gmail.com> wrote: > Hi Andrew, > > Here is what I get: > > >>> File("mesh.pvd")<<mesh.coordinates > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > AttributeError: 'module' object has no attribute ‘coordinates' > > What could be the issue? > > On 09 Dec 2015, at 15:36, Andrew McRae <A.T.T.McRae(a)bath.ac.uk> wrote: > > Hi David, > > The mesh for this is BoxMesh. For documentation, type '? BoxMesh' at a > python prompt, after importing firedrake, or see line 475 onwards of > https://github.com/firedrakeproject/firedrake/blob/master/firedrake/utility… > > In your case, you want > BoxMesh(nx, ny, nz, 1.0, 1.0, 2.0), where nx, ny and nz are the number of > cells in the x, y and z direction respectively. Ideally (see below), each > cuboid is divided into 6 tetrahedra, so the total number of cells is > 6*nx*ny*nz, so you can control this exactly. > > Unfortunately, there is a trap: if you want cells whose x, y and z > dimensions are very different, the mesh generator will generate extra > points. > > With the dimensions you gave above, if you have nx = 10, ny = 10, nz = 20, > you get what you expect - lots of cubes, each divided into 6 tetrahedra. > > However, if you have nx = 5, ny = 5, nz = 100, you get something > completely different (lots of small cells). > > You can visualise the mesh by using > File("mesh.pvd") << mesh.coordinates > and opening the file in Paraview in 'Wireframe' mode. > > There's a very easy workaround, so do reply if this is a problem for you. > > Best, > Andrew > > On 9 December 2015 at 14:15, Angwenyi David <kipkoej(a)gmail.com> wrote: > >> Dear all, >> >> I would like to solve a 3d Helmholtz equation in a domain 0 <= x <= 1, 0 >> <= y <= 1, 0 <= z <= 2 tessellated into any number of tetrahedra. Is this >> possible within Firedrake, and if yes, what is the mesh name? >> >> David >> _______________________________________________ >> 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 > > >

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Re: [firedrake] Tetrahedral mesh
by Andrew McRae 09 Dec '15

09 Dec '15

Hi David, The mesh for this is BoxMesh. For documentation, type '? BoxMesh' at a python prompt, after importing firedrake, or see line 475 onwards of https://github.com/firedrakeproject/firedrake/blob/master/firedrake/utility… In your case, you want BoxMesh(nx, ny, nz, 1.0, 1.0, 2.0), where nx, ny and nz are the number of cells in the x, y and z direction respectively. Ideally (see below), each cuboid is divided into 6 tetrahedra, so the total number of cells is 6*nx*ny*nz, so you can control this exactly. Unfortunately, there is a trap: if you want cells whose x, y and z dimensions are very different, the mesh generator will generate extra points. With the dimensions you gave above, if you have nx = 10, ny = 10, nz = 20, you get what you expect - lots of cubes, each divided into 6 tetrahedra. However, if you have nx = 5, ny = 5, nz = 100, you get something completely different (lots of small cells). You can visualise the mesh by using File("mesh.pvd") << mesh.coordinates and opening the file in Paraview in 'Wireframe' mode. There's a very easy workaround, so do reply if this is a problem for you. Best, Andrew On 9 December 2015 at 14:15, Angwenyi David <kipkoej(a)gmail.com> wrote: > Dear all, > > I would like to solve a 3d Helmholtz equation in a domain 0 <= x <= 1, 0 > <= y <= 1, 0 <= z <= 2 tessellated into any number of tetrahedra. Is this > possible within Firedrake, and if yes, what is the mesh name? > > David > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Tetrahedral mesh
by Angwenyi David 09 Dec '15

09 Dec '15

Dear all, I would like to solve a 3d Helmholtz equation in a domain 0 <= x <= 1, 0 <= y <= 1, 0 <= z <= 2 tessellated into any number of tetrahedra. Is this possible within Firedrake, and if yes, what is the mesh name? David

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boundary conditions on a mixed function space
by William Booker 09 Dec '15

09 Dec '15

Dear Firedrakers, I've been trying to implement 0 dirichlet boundaries on a mixed function space that includes a vector space #Set up boundary conditions bcv_x = DirichletBC(W.sub(0).sub(0), Constant(0), method="geometric") bcv_z = DirichletBC(W.sub(0).sub(1), Constant(0), method="geometric") but I get back AttributeError: 'VectorFunctionSpace' object has no attribute 'sub' I thought we were meant to use sub twice to refer first to the function space component and then to the vector component. Also, would this be a correct approach for implementing no normal flow boundaries or is there a more appropriate method to use. Thanks Will

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