All Questions
0
votes
0answers
1 views
Fenics, Sine Gordon equation - time independent
Is there a code for this equation θ^2u/θx^2+θ^2u/θy^2 = sin(u) or for sine gordon equation in two dimensions because i want to change some boundary values to see the results?
0
votes
0answers
5 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 rectangular beam and want to apply Dirichlet bc (u ==0) in left side of a beam in ...
6
votes
2answers
47 views
Genetic algorithm vs conjugate gradient method
I am trying to optimize some force-field parameters in a molecular framework so that the result of simulation comes as close as it can to the experimental structure.
In the past, I have written a ...
2
votes
0answers
27 views
How to apply periodic boundary conditions to a Raviart-Thomas finite element space in Fenics?
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, ...
-1
votes
1answer
52 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 ...
7
votes
3answers
53 views
Optimal ODE method for fixed number of RHS evaluations
In practice, the runtime of numerically solving an IVP
$$
\dot{x}(t) = f(t, x(t)) \quad \text{ for } t \in [t_0, t_1]
$$
$$
x(t_0) = x_0
$$
is often dominated by the duration of evaluating the ...
1
vote
0answers
9 views
How do I implement a custom kernel in scikit GP?
http://scikit-learn.org/0.13/modules/gaussian_process.html#correlation-models
I'd like to write a kernel. How can I do that?
1
vote
1answer
38 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 ...
0
votes
1answer
47 views
SVD regularization - ray 2D tomography
Sunny day today, isn't it? Please, I need help with my problem. I have written a program to do 2D ray tomography, according to this paper.
For the result, I use formula (4.15) from the paper. Now I ...
7
votes
3answers
148 views
Is CFD used in animations / movies / art?
This is not a technical question, and is asked just out of curiosity.
Are CFD simulations used in animation movies? (something like shallow water equations, explosion problem etc.)
In other words, ...
-2
votes
0answers
24 views
Stepsize scheme foroptimizing penalty function method [closed]
ii was told to work on various stepsize schemes for optimizing penalty function method. But i got confused on what to do
2
votes
0answers
23 views
Benchmarks or generic configurations for optimal flow control
I am about to test my algorithms for solving optimal control problems of type:
Find an input $u$, such that for a time interval $(0,T]$ the cost functional
$$J(v,u) = \mathcal M(v(T)) + ...
0
votes
0answers
12 views
DFT/FFT: What did N stand for again? [migrated]
So if I have an image of the size: 1920×1080 and I want to apply a convolution filter of 3x3. What is N in this case?
0
votes
1answer
42 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 ....
...
6
votes
1answer
78 views
Why is it difficult to numerically solve multi-electron time-dependent Schrödinger's equation
It seems that people usually use the Single Active Electron (SAE) approximation to deal with a multi-electron system, transforming the problem into a single electron problem. For example, in ...
5
votes
1answer
16 views
The etymology of “Umbrella Sampling”
I am just wondering where the term Umbrella Sampling came from. Is there another meaning of literal "umbrella" in physics or mathematics?
7
votes
2answers
63 views
Which preconditioners (and solver) in PETSc for indefinite symmetric systems should I use?
My system is a symmetric FE problem with lagrange multipliers (e.g. incompressible Stokes' flow):
\begin{pmatrix}A & B^T \\ B & C\end{pmatrix}
where $C = 0$ is the typical case (I have even ...
3
votes
0answers
36 views
Prediction model on GPU
I am doing a small project at school. I have done my code implementations in CUDA and did some performance measurements with real values, i.e. running the program with different number of threads, ...
0
votes
1answer
38 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 ...
5
votes
2answers
73 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 ...
1
vote
0answers
25 views
Error bars for pair-correlation function
I have obtained some data from neutron diffraction for some material samples. The "rawest" form of the data is the structure function $S(Q)$.
We can choose a variety of different Q-maxes when ...
4
votes
1answer
57 views
Conservative finite-difference expression for the advection equation
Following on from the earlier question I am trying to derive a finite-difference scheme for the advection equation which is conservative. It was suggested that for advection equation with variable ...
0
votes
1answer
39 views
Spring damper model does not work very well
I'm trying to model a spring damper system from a tutorial that I've found on this site.
If I use the exact same parameters as the ones in the tutorial the system is not stable. I've downloaded the ...
4
votes
1answer
42 views
Is stabilization of energy equation needed when momentum equation needs it?
When SUPG/PSPG stabilization is added to momentum equation of flow problem, is needed stabilization for energy equation also? I would guess that when stabilization for velocity works fine so one gets ...
1
vote
0answers
8 views
Combining trend estimation and constrained Marquart fit
This title certainly needs some clarification: I need to compute parameters $a_i$ for a helper function $f(\vec{a};k)$ (for grid interpolation) which is fitted to a number of values $y_k$ which are ...
3
votes
2answers
44 views
Trajectory Planning: Polynomials as universal, integrable approximation functions?
I'd like to program a trajectory planner, let's say for a robot, and I can pass acceleration commands to the robot, the robot can move in one dimension. The outcome of the planner is now a vector with ...
2
votes
1answer
45 views
Minimal surface solution in Python
Note: this question was also posted in StackOverflow and math.stackexchange.
I have a set of 3D points defining a 3D contour, as shown below. The points in this contour lie in their best-fit plane ...
9
votes
1answer
71 views
Can the advection equation with variable velocity be conservative?
I am trying to understand the advection equation with variable velocity coefficient a bit better. In particular I don't understand how the equation can be conservative.
The advection equation,
$$
...
2
votes
1answer
25 views
Creating a local vector in a parallel PETSC program
In one of my PETSc programs, I need a processor to access values from another processor.
So in the PETSc FAQ's this issue has been briefly addressed here.
To create a local vector, I tried this
...
8
votes
1answer
93 views
Does anyone use software estimation methods in their computational science research?
At work, I essentially function as an independent consultant. For management and customers, I need to estimate the amount of time it will take to develop software as part of my computational science ...
1
vote
0answers
17 views
Accurate force-field for MD
I am still a fairly new graduate student, and I am having trouble simulating a metal-organic framework. I am currently using UFF (I implemented it for LAMMPS), and it works well for some MOFs, but ...
3
votes
1answer
53 views
Compute spatial second derivatives in Isogeometric analysis
Motivation:
In isogeometric analysis, state variables(e.g. displacement) are defined in the parametric domain, which can be mapped to the physical domain by $\boldsymbol{\xi}\mapsto \boldsymbol{x}$ ...
2
votes
0answers
39 views
Explicit 4th order space wave equation not stable implementation?
The explicit 4th order discretization for the 2D scalar wave equation is given by:
\begin{eqnarray}
U_{jk}^{n+1} = \left( \frac{\Delta t V_{jk} }{\Delta s} \right) ^2 \left( \sum_{a=-N}^N w_a ...
1
vote
0answers
16 views
Simulation of asymmetric structures (occupancy = 0.5) unstable
I am trying to simulate a metal-organic framework in LAMMPS using the UFF potential. It's working quite well for some structures where all molecules have an occupancy of 1.
However, when I have a ...
3
votes
2answers
70 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 ...
0
votes
0answers
38 views
Pre-stressing within fenics
How can I go about incorporating pre-stressing into a code using fenics. In particular what I have is a code which creates a mesh, applies external forces and calculates the displacement based on min ...
1
vote
0answers
56 views
What methods exist to solve for the fluid flow past a cylinder using finite differences on a Cartesian grid?
I'm interested in finite-difference approaches to the incompressible Navier-Stokes equations that can handle complex geometry without the use of an unstructured mesh or a non-Cartesian grid. To be ...
9
votes
2answers
105 views
Oscillations in singularly perturbed reaction-diffusion problems with finite elements
When FEM-discretizing and solving a reaction-diffusion problem, e.g.,
$$
- \varepsilon \Delta u + u = 1 \text{ on } \Omega\\
u = 0 \text{ on } \partial\Omega
$$
with $0 < \varepsilon \ll 1$ ...
11
votes
1answer
70 views
Using fixed point iteration to decouple a system of pde's
Suppose I had a boundary value problem:
$$\frac{d^2u}{dx^2} + \frac{dv}{dx}=f \text{ in } \Omega$$
$$\frac{du}{dx} +\frac{d^2v}{dx^2} =g \text{ in } \Omega$$
$$u=h \text{ in } \partial\Omega$$
My ...
3
votes
2answers
96 views
What is the Complexity of MATLAB operations
I'm trying to analyze the complexity of MATLAB code I wrote.
I'm trying to figure out how much (in terms of $O$ or $\Theta$) to give functions like find, matrix ...
1
vote
1answer
27 views
CFD (Fluent) define a inlet for a tidal basin
I'm still pretty new in the CFD modelling world.
Can anyone advise me how to define a inlet for a tidal basin in Fluent?
The water level and the velocity at the inlet vary in time due to the tide ...
4
votes
2answers
119 views
Computing matrix exponential with PETSc/SLEPc
My question is basically the best way to compute the matrix exponential in parallel. I've got a sequential code written in Python (https://github.com/hadsed/AdiaQC) and I need to extend it to run in a ...
1
vote
1answer
41 views
What is a “wake” in the context of CFD?
I am getting into computational fluid dynamics (CFD). One of my professors mentioned that a cylindrical wake would be a good starting point to learn about turbulence modelling when using CFD software. ...
4
votes
2answers
81 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 ...
0
votes
1answer
41 views
xml Mesh format -Fenics
I imported an xml file format and the nodal connectivty seems to be different than what FeniCS usually follow..
Is it possible to sort the nodes or element connectivity same as Fenics ???because ...
5
votes
2answers
90 views
How many cells/elements do I need?
I'm relatively new in the CFD modelling and I'm making a VOFmodel of a rectangular box (lxwxh 120x80x8m) with an inlet (wxh 10x8) at the long side. The pressure outlet is the upper-face of the box ...
4
votes
1answer
63 views
Solving linear systems by fft
I read in a paper and also at wiki that we can solve the system
$$Ax=B$$
by Fast Fourier Transform, where $A$ is a circulant matrix. The solution is
...
4
votes
1answer
75 views
Integration of an indefinite integral: matlab precision problem
The integral I need to evaluate is:
$$ \int_x^{\infty} \frac{t^n}{e^{t} -1} dt $$
After some research I found a paper saying,
The numerical values of the two integrals [...] are easily ...
2
votes
2answers
84 views
Earth and Moon computer simulation
So I want to simulate the solar system but want to start simple with one orbiting body. However, I never did anything like this before and was wondering if anyone here could give me some hints.
...
3
votes
1answer
77 views
Early work on inverse problems
Long time ago I came across with a paper that covered early theoretical work (first half of 20th century) in the field of inverse problems. I remember there was a reference to a paper which proved ...
