Questions tagged [fenics]

Questions about the finite element method software FEniCS and its subpackages (Dolfin, UFL, FFC).

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Recommendations on FEM software for implementing Nitsche's method on interfaces between matching meshes?

Suppose: I have two domains, $\Omega_{1} = [0, 1/2] \times [0, 1]$ and $\Omega_{2} = [1/2, 1] \times [0, 1]$. The domains share an interface $\Gamma = \{1/2\} \times [0, 1] = \partial\Omega_{1} \cap \...
Geoff Oxberry's user avatar
1 vote
1 answer
662 views

Tensor notation in fenics [closed]

Within Fenics what ordering is used for storing vectors as upper triangular matrices? Th:e question really is I define a green Lagrange strain tensor in the following way: ...
Nick's user avatar
  • 148
3 votes
2 answers
695 views

Integrating an Ordinary Differential Equation over a domain in Finite Element Methods

I'm trying to get a deeper understanding of the Finite Element Method (FEM) to better understand what I do in COMSOL and FEniCS. The sketch below shows the problem that I want to solve in FEM. The ...
seb's user avatar
  • 974
2 votes
1 answer
680 views

Basic Finite Element Method (FEM) question: assembly and re-assembly

I'm reading up on the Finite Element Method (Zienkiewicz's Book), so I understand better what I'm doing in FEniCS and COMSOL. Currently, I'm wondering about this: Using FEM to solve fluid flow ...
seb's user avatar
  • 974
2 votes
1 answer
587 views

PETSc Krylov Subspace and nullspace

How is the nullspace correction implemented in the PETSc conjugate gradient solver? I searched the source code and documentation, but could not find references on the actual implementation. For ...
jmk's user avatar
  • 123
3 votes
1 answer
1k views

weak formulation of coupled pdes for fenics

I am trying to implement the following system of time-dependent, coupled nonlinear pdes in FEniCS: $$\partial_{t}\rho+2\left(\nabla\rho\nabla\phi+\rho\nabla^{2}\phi\right)+2\sigma\rho\left(\rho-1\...
Andrei's user avatar
  • 203
2 votes
1 answer
2k views

time-dependent nonlinear pde in fenics

I am interesting in solving the following nonlinear, time-dependent pde in 2 spatial dimensions (complex Gross-Pitaevskii eq): $$i \frac{\partial \psi}{\partial t} = \left[ -\nabla^2 + (1-i \sigma)(|\...
Andrei's user avatar
  • 203
0 votes
1 answer
1k views

defining subdomains in FEniCS (Python) using obtained (solved) variable [closed]

I'd very much appreciate if you could help me out with this as I think I'm missing something simple out or should be using alternate syntax: I am running the following Python code in FEniCS, where I ...
micawber's user avatar
3 votes
2 answers
2k views

Subdomain Integrals in Fenics

I'd like to compute $u(y) = \int f(x,y) dx$, but don't see a really efficient way to do this in FEniCS. My first thought was to just assemble(f*v*dx) for two different meshes. (try1, below), but it ...
David M. Rogers's user avatar
3 votes
2 answers
110 views

Quantification of non-stationarity of PDE solution

Suppose I have a time-dependent PDE discretized by the Rothe method and FEM, like $$ \int_{\Omega} k^{n+1/2}(u^{n+1}-u^{n}) v \;\mathrm{d}x = F^{n+1/2}(u^{n+1},u^n)[v] \quad \forall v\in V_h^n. $$ ...
Jan Blechta's user avatar
3 votes
1 answer
589 views

Implementation of a contraction force in Fenics

Is there any way to implement an element wise contraction force (i.e., a force which causes the FEs themselves to contract onto themselves)? For example this would happen when something dehydrates. ...
Nick's user avatar
  • 148
4 votes
2 answers
2k views

FEniCS: importing mesh along with material and boundary data

Which is the preferred way to import into a FEniCS (python) program a mesh which was generated in an external generator which provides sub-domain and boundary markers? I was using MeshData->...
Jacek's user avatar
  • 41
6 votes
1 answer
2k views

FEniCS CFD work-flow for complex geometries

I have COMSOL and the CFD package therein available, which provides me with an all-in-one solution for solving CFD problems. I have modeled and solved the geometry shown in the pictures below, which ...
seb's user avatar
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4 votes
1 answer
146 views

Assembling FE tensors using different quadrature degrees

Assume we have few terms contributing to element tensor and each requires different quadrature degree to be integrated exactly. Does it generally worth using different quadrature degrees for each term ...
Jan Blechta's user avatar
3 votes
2 answers
1k views

Flux across a non-boundary line segment in FEniCS

I am solving an elliptic boundary value problem on a subset of the rectangle [-1,1]x[-1,1]. The domain contains the line segment x=0, however this does not need to be a part of the boundary, so it is ...
Ian's user avatar
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15 votes
2 answers
3k views

FeniCS: Visualizing high order elements

I've just started messing around with FEniCS. I am solving Poisson with 3rd order elements and would like to visualize the results. However, when I use plot(u), the visualization is just a linear ...
Truman Ellis's user avatar
2 votes
1 answer
411 views

Mixed FEM vector indices of pressure and velocity in FEniCS

Looking at the stokes-iterative demo of FEniCS, after solving the linear system using U = Function(W) solver.solve(U.vector(), bb) the solution ...
user4451's user avatar
6 votes
0 answers
687 views

Stochastic Galerkin projection approach for using generalized polynomial chaos expansion (GPCE) in solving PDE

I want to know if there is any way to define the test and trial function in the way that I want instead of using the default functions. So if I want define the polynomial and basis and coefficient, ...
Bahram's user avatar
  • 111
0 votes
2 answers
177 views

Speed up DG FunctionSpace evalutation [closed]

today I tried some evaluation on a DG function space (Fenics 1.2.0). In my calculations I need to use meshes with a large number of cells (~10mio). At the moment it takes a very long time to create a ...
Sebastian's user avatar
1 vote
2 answers
1k views

How can I build a mesh with holes for use in FEniCS?

This is my first time using FEniCS. I am trying to solve an elliptic PDE, fairly similar to the Laplace equation, on a rectangle with two holes in it. The holes are level sets of an energy function, ...
Ian's user avatar
  • 173
11 votes
2 answers
3k views

Discontinuous Galerkin / Poisson / Fenics

I am trying to solve the 2D Poisson equation using the Discontinuous Galerkin method (DG) and the following discretization (I have a png file but I am not allowed to upload it, sorry): Equation : $$\...
micdup's user avatar
  • 115
2 votes
4 answers
2k views

Simple FEniCS problem shape mismatch

This presentation by the Imperial College in London has a nice example in it, on page 8, Burgers Equations. The first part of their code reads like this: ...
seb's user avatar
  • 974
7 votes
2 answers
2k views

FEniCS: boundary conditions for electrostatic problems with dielectrics

I carefully read all circa 70 pages of FEniCS tutorial and I still do not understand how to solve electrostatic problems when I have materials with different dielectric constant. The self contained ...
facetus's user avatar
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7 votes
2 answers
6k views

FEniCS: how to specify boundary conditions on a circle inside 2D mesh

I would like to numerically find a mutual capacitance of two stripes of metal on the opposites sides of a cylinder. The problem is obviously a 2D Laplace equation. I would like to find the potential ...
facetus's user avatar
  • 358
6 votes
1 answer
920 views

FEniCS: how to access coordinates when writing an equation for a trial function

I need to solve the following equation in FEniCS: $$ \boldsymbol{\nabla} \cdot \begin{pmatrix} f(y)\frac{\partial u}{\partial x} - g(x,y)\frac{\partial u}{\partial y} \\ - g(x,y)\frac{\partial u}{\...
facetus's user avatar
  • 358
4 votes
4 answers
8k views

Fenics: msh to xml conversion

I generated a mesh file in gambit and wanted to convert it to xml format. I tried the code below, but there is no output. ...
nickrocks's user avatar
  • 117
2 votes
4 answers
454 views

2d-mini element-can't use sub(0),but bubble element is ok

My program (in Python, using FEniCS): ...
jiangliuer2013's user avatar
3 votes
1 answer
567 views

Fenics: time-independent Sine-Gordon equation

Is there a code for the equation $$ \frac{\partial^2u}{\partial x^2}+\frac{\partial^2u}{\partial y^2} = \sin(u) $$ or for the sine gordon equation in two dimensions because I want to change some ...
jessie's user avatar
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4 votes
1 answer
4k views

Fenics: Meshfunction usage

I am confused most of the time with the application of boundary conditions in Fenics. Suppose I have an xml mesh for a rectangular beam and want to apply Dirichlet BC ($u =0$) on the left side of the ...
nickrocks's user avatar
  • 117
2 votes
0 answers
805 views

How to apply periodic boundary conditions to a Raviart-Thomas finite element space in Fenics? [closed]

I'm trying to use periodic boundary conditions within a Raviart-Thomas finite element space in Fenics (dolfin 1.2.0) in a Ubuntu 12.04 (amd64) machine (with python 2.7). If other FE space is used, ...
maprieto's user avatar
-3 votes
1 answer
688 views

Fenics : boundary condition

`I am working on a problem found here " http://www.caesarsystems.co.uk/NAFEMS_benchmarks/le10.html" ..I am really confused about the boundary conditions and tried my level best to compute it but ...
nickrocks's user avatar
  • 117
2 votes
1 answer
912 views

Fenics : Elementwise stress computation

In a elastodynamics problem, I define the stress as def sigma(v): return 2.0*mu*sym(grad(v)) + lmbda*tr(sym(grad(v)))*Identity(v.cell().d) I have computed ...
nickrocks's user avatar
  • 117
0 votes
1 answer
555 views

Fenics : looking forward to compute displacements at nodes

I just went through the Fenics book to get the nodal displacements and tried this code .... ...
nickrocks's user avatar
  • 117
1 vote
1 answer
344 views

Fenics: problem with the mesh generation

while executing my script i get this error Traceback (most recent call last): File "/media/oss/Fenics/demo/box_3delasticity.py", line 33, in mesh = Box (0, 0, 0, 1, 1, 1, 1, 1, 1) File "/usr/...
nickrocks's user avatar
  • 117
7 votes
3 answers
6k views

Tutorial for flow around a cylinder in FEniCS

I am continuing my dive into computational fluid dynamics. I would like to build a simple test case for modelling the flow around a cylinder in FEniCS and then continue to model turbulence in order to ...
seb's user avatar
  • 974
5 votes
2 answers
1k views

FEniCS: custom quadrature rule

For the numerical integration of reaction terms in my PDE on a 2D triangular mesh, I would like to use the scheme $$ \int_T \Phi(x) \approx \frac{|T|}{3} (\Phi(x_0) + \Phi(x_1) + \Phi(x_2)) $$ where ...
Nico Schlömer's user avatar
4 votes
2 answers
507 views

Poiseuille flow

I have probably a very stupid problem. I can't solve a simple Poiseuille flow in a straight 2-D channel driven by a pressure drop. Results are complete nonsense. (Setting zero pressure on the outflow ...
Marek N.'s user avatar
9 votes
0 answers
427 views

Simple turbulence model appropriate for buoyancy-driven cavity like problem

Which turbulence model is suitable for resolving incompressible buoyancy-driven flow of a fluid within an cylindrical ampoule? I prefer turbulence model which is sufficiently simple so that fully ...
Jan Blechta's user avatar
11 votes
3 answers
4k views

Poisson equation: Impose full gradient as boundary condition via Lagrange multipliers

I have a physical problem governed by the Poisson equation in two dimensions $$ -\nabla^2 u = f(x,y), \; in \; \Omega $$ I have measurements of the two gradient components $\partial{u}/\partial{x}$ ...
Markus's user avatar
  • 213
4 votes
1 answer
2k views

Fenics, initialize vector of degrees of freedom for function

With the move away from launchpad I hope this is the right place for this question. Is there a way to initialize the DOFs for a function? generated by u = Function(V) When I run a code which I ...
Nick's user avatar
  • 148
5 votes
1 answer
1k views

Compute lengths of the longest edge of each cell

Having mesh = UnitSquareMesh(2, 2) Q = FunctionSpace(mesh, 'DG', 0) this works as expected ...
Jan Blechta's user avatar
4 votes
0 answers
539 views

Fenics: Result of Steady state dynamic linear elastic doesn't match with actual values

I solved the steady state dynamic linear elastic model in a solid. My equation is a function of frequency and the strong form is: $$\operatorname{div}(\operatorname{stress}(\vec x, w)) + w^2 \rho u( \...
Bahram's user avatar
  • 111
4 votes
1 answer
155 views

compute max(||u||) for vector field

Given a vector-valued Dolfin function u from the function space V*V with ...
Nico Schlömer's user avatar
3 votes
1 answer
299 views

Fast function evaluation on a grid

I am trying to calculate a 3D Function f on a large set of points, say a uniform cubic grid. Besides, the cubic grid points do not coincide with the mesh vertices where the Function f is defined. For ...
user4232's user avatar
4 votes
4 answers
2k views

FEniCS : How to interpolate data at vertices of (3D) cells?

I am trying to get an interpolation function $f$ (in 3D) at all vertices of cells. I extract all vertices of cells and then I assign the value to each vertex: if it's in a sphere of radius $R$, then I ...
Paul S.'s user avatar
  • 41
2 votes
2 answers
611 views

FEniCS: check if function is globally greater than 0

Given a Dolfin Function u on a mesh, I'd like to check if it is greater than 0 throughout the mesh. I noticed that the ...
Nico Schlömer's user avatar
4 votes
2 answers
1k views

CFD: multiphase flow modeling of a laminar flow reactor

I am planning to model the laminar flow reactor shown in the picture below using computational fluid dynamics (CFD). The laminar flow reactor is used to study a multiphase flow: a layer of sheath air ...
seb's user avatar
  • 974
7 votes
2 answers
4k views

FEniCS: separate boundary conditions in normal and tangential direction of mesh boundary

Given a vector-valued PDE, I'd like to enforce the boundary conditions $$ \vec{n}\cdot u = g\\ \vec{n}\cdot \nabla (\vec{t}\cdot u) = 0 $$ on the solution $\vec{u}$. If the boundary happens to align ...
Nico Schlömer's user avatar
3 votes
2 answers
1k views

FEniCS: extracting points from a cell

I'd like to loop over all edges of a simplex (in a mesh). To this end: How can I extract the the points from a cell? This is for the eval method of a C++ ...
Nico Schlömer's user avatar

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