August 2018 - firedrake - imperial.ac.uk

Can Firedrake handle non-constant Jacobian elements?
by Mohammad Sarraf Joshaghani 09 Aug '18

09 Aug '18

Hello, I am trying to run a 3D problem with HEX mesh, using RT0 formulation. I am wondering if RT0 (extruded RTCF) could be used for 3D non-constant Jacobian elements in Firedrake? I attached a sample of mesh for clarification. Thank you for your help. Best Regards, Sarraf

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Adaptive refining
by Amireh Mousavi 03 Aug '18

03 Aug '18

Dear all, I'm trying to use adaptive algorithm in Firedrake. Because it's essential in my thesis. I have problem with marking cell and locally refining step. The following is my test code for one iteration: REFINE_RATIO = 0.50 # Refine 50 % of the cells in each iteration mesh = UnitSquareMesh(4, 4) BDM = FunctionSpace(mesh, "BDM", 1) DG = FunctionSpace(mesh, "DG", 0) W = BDM * DG sigma, u = TrialFunctions(W) tau, v = TestFunctions(W) x, y = SpatialCoordinate(mesh) f = Function(DG).interpolate( 10*exp(-(pow(x - 0.5, 2) + pow(y - 0.5, 2)) / 0.02)) a = (dot(sigma, tau) + div(tau)*u + div(sigma)*v)*dx L = - f*v*dx bc0 = DirichletBC(W.sub(0), as_vector([0.0, -sin(5*x)]), 1) bc1 = DirichletBC(W.sub(0), as_vector([0.0, sin(5*y)]), 2) w = Function(W) solve(a == L, w, bcs=[bc0, bc1]) sigma, u = w.split() expr = (div(sigma)+f)*(div(sigma)+f) P0 = FunctionSpace(mesh, "DG", 0) Re = project(expr, P0) coeffs = Re.dat.data ss = sorted(coeffs, reverse=True)[int(len(coeffs)*REFINE_RATIO)] #-------------------------The followin are marking and refining which work in Dolfin --------------------------- cell_markers = MeshFunction("bool", mesh, mesh.topology().dim()) for c in cells(mesh): cell_markers[c] = coeffs[c.index()] > ss mesh = refine(mesh, cell_markers) 1) How can I use the loop over the cells in Firedrake? ( for c in ?) 2) Is there a way to refine some marked cell in Firedrake? Your answer will be greatly appreciated. All the best, Amireh

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.array()
by Amireh Mousavi 02 Aug '18

02 Aug '18

Dear Firedrake team, i'm trying to get u*v*dx as a array which each component is amount of the integral on each element. I want to do that in order to compute error indicator. In dolfin implementation it be done like: assemble(u*v*dx).array() Is there a way to do this in Firedrake? Runing the above code in Firedrake gives: AttributeError: 'numpy.float64' object has no attribute 'array' Thank you in advance. Best, Amireh

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complex?
by Colin Cotter 01 Aug '18

01 Aug '18

Dear FD, Upon running the following code: from firedrake import * n = 20 mesh = UnitSquareMesh(n,n) V = FunctionSpace(mesh,"CG",1) I get the message at the bottom of this email. Does this mean I have incorrectly built a complex branch? (I built it by running the install script from the jenkinsfile in the complex branch, then changing to the complex branch.) all the best --cjc Traceback (most recent call last): File "complex_helmholtz.py", line 4, in <module> V = FunctionSpace(mesh,"CG",1) File "<decorator-gen-530>", line 2, in FunctionSpace File "/home/cjc1/firedrake-complex/firedrake/src/PyOP2/pyop2/profiling.py", line 60, in wrapper return f(*args, **kwargs) File "/home/cjc1/firedrake-complex/firedrake/src/firedrake/firedrake/functionspace.py", line 118, in FunctionSpace element = make_scalar_element(mesh, family, degree, vfamily, vdegree) File "/home/cjc1/firedrake-complex/firedrake/src/firedrake/firedrake/functionspace.py", line 40, in make_scalar_element mesh.init() File "/home/cjc1/firedrake-complex/firedrake/src/firedrake/firedrake/mesh.py", line 993, in init self._callback(self) File "/home/cjc1/firedrake-complex/firedrake/src/firedrake/firedrake/mesh.py", line 1335, in callback (self.num_vertices(), geometric_dim)) File "firedrake/dmplex.pyx", line 851, in firedrake.dmplex.reordered_coords ValueError: Buffer dtype mismatch, expected 'PetscReal' but got 'complex double' -- Colin Cotter Department of Mathematics Imperial College London I don’t expect a reply to this email from you outside of your normal working hours. http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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