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5
votes
1answer
426 views

Applying Dirichlet b.c. to the Eigenvalue-Problem

If you use a FEM (on the variational formulation), you can discretize some continuous eigenvalue problem, $$L u = \lambda u \ \ \text{on} \ \Omega,$$ into some discrete, generalized eigenvalue problem,...
5
votes
2answers
417 views

Solving Poisson equation with current BC using FEM

I have a 3-dimensional domain D, with 3 types of BC which I am trying to solve the Poisson equation on. $$-\nabla \cdot (\sigma(x,y,z)\nabla u)=0$$ Insulator (Neumann BC) Electrode set at some ...
5
votes
5answers
2k views

How do I create an animation from a 2D model or dataset?

I found the following thread in the physics stackexchange where I saw the video called output attached to the main post. The video can be found here. How would I go about creating such an animation?
5
votes
2answers
2k views

implementing higher order derivatives for finite element

I am implementing higher order derivatives for FEM. Example, to solve a Poisson problem, biharmonic or triharmonic PDE one needs first, second or third order derivatives respectively. As usually ...
4
votes
2answers
1k views

Line search for Newton method

If we want to solve nonlinear minimization problem $$\min_{x} f(x),$$ making least-squares assumption and using Gauss-Newton method so that at k$th$ iteration we have: $$J_k^T J_k p_k = - J_k^T ...
25
votes
3answers
1k views

Why is the time dimension special?

Generally speaking, I've heard numerical analysts utter the opinion that "Of course, mathematically speaking, time is just another dimension, but still, time is special" How to justify this? In ...
18
votes
5answers
6k views

State of the Mac OS in Scientific Computing and HPC

Back towards the dawn of OS X, there seemed to be a great deal of hubbub, at least in the Mac world (I was nowhere near scientific computing at the time) about the Mac OS as a platform for scientific ...
17
votes
5answers
909 views

How to address numerical non-associativity for parallel reduction?

A parallel reduction assumes that the corresponding operation is associative. This assumption is violated for addition of floating point numbers. You might ask why I care about this. Well, it makes ...
16
votes
2answers
821 views

How can I choose a good Riemann solver when numerically solving a system of hyperbolic PDEs?

Many numerical methods for hyperbolic PDEs are based on the use of Riemann solvers. Such solvers are essential for accurately capturing shock waves. There are a range of such solvers available for ...
14
votes
6answers
1k views

Approximate spectrum of a large matrix

I want to compute the spectrum (all the eigenvalues) of a large sparse matrix (hundreds of thousands of rows). This is hard. I am willing to settle for an approximation. Are there approximation ...
13
votes
1answer
1k views

Why is pinning a point to remove a null space bad?

A Poisson equation with all Neumann boundary conditions has a single constant dimensional null space. When solving via a Krylov method, the null space can be removed either by subtracting the mean of ...
13
votes
1answer
355 views

How to construct well-balanced finite volume and discontinuous Galerkin methods for hyperbolic PDEs with source terms?

Source terms, such as those due to bathymetry in the shallow water equations, need to be integrated in a special way in order to preserve physical steady states. Is there a general way to construct ...
12
votes
2answers
3k views

What is the corresponding LAPACK function behind Matlab [Q,R,E]=qr(A)?

I currently trying to cheaply compute a good rank estimate for a matrix $A$. Therefore I compute a columnt pivoting QR decompostion using [Q,R,E]=qr(A) in ...
12
votes
1answer
1k views

How exactly does the *full* multigrid algorithm run?

So I understand (or at least I believe I do) how a V-cycle runs. I've written in Matlab the 1-D, recursive version of a V-cycle. However, when I ran my code for FMG, my solution wasn't converging. I ...
12
votes
1answer
403 views

Costs of lookups versus calculations

I am interested in setting up calculations to check if a distance criterion is satisfied: that is, the distance between a vector ${\bf x}_i$ and anther vector ${\bf x}_j$ should be less than some ...
11
votes
2answers
2k views

How is the SVD of a matrix computed in practice

How does MATLAB, for instance, calculate the SVD of a given matrix? I assume the answer probably involves computing the eigenvectors and eigenvalues of A*A'. If ...
11
votes
3answers
1k views

Least squares approximation question

I am taking a course on scientific computation, and we just went over least squares approximation. My question is specifically about approximating using polynomials. I understand that if you have n+1 ...
10
votes
3answers
1k views

Can compressible flow solvers be used to solve incompressible flow?

I know that incompressible and compressible flow solvers are specifically designed to solve different types of problems with different fluid properties/flow conditions. Clearly, among the advantages ...
10
votes
1answer
611 views

How to assemble and solve a matrix system in parallel from values generated in different processors?

I am solving a multiscale problem using the Heterogeneous Multiscale Method (HMM). Essentially, my particular procedure uses the following iterative process: Solve many local matrix systems. ...
10
votes
5answers
6k views

How are the Voronoi Tesselation and Delaunay triangulation problems duals of each other?

I have always been told that the Voronoi diagram is the dual of the Delaunay triangulation problem. In what sense can they be duals of each other? I thought that dual problems (i.e. in linear ...
10
votes
2answers
2k views

Higher-order numerical integration on a triangle/tetrahedron/simplex

Let $T$ be a triangle and let $f$ be a smooth function on $T$. We can use mid-point quadrature $\int f dx \approx |T|\cdot f(x_M)$, where $x_M$ is the middle-point of $T$. Can you provide me with (a ...
10
votes
2answers
736 views

Trace An Isoline of an Expensive 2D Function

I have a problem similar in formulation to this post, with a few notable differences: What simple methods are there for adaptively sampling a 2D function? Like in that post: I have a $f(x,y)$ and ...
10
votes
3answers
3k views

How to construct a prolongation and restriction operator for an algebraic multigrid solver?

I am trying to solve a linear system of equations that is sparse, but lacks any kind of banded structure. I have heard that there is a way to extend the principles of a multigrid solver for implicit ...
9
votes
4answers
4k views

Order of MATLAB FFT frequencies

This wikibook states that the output of MATLAB's FFT corresponds with the wavenumbers ordered as: $$k=\left\{0,1,...,\frac{n}{2},-\frac{n}{2}+1,-\frac{n}{2}+2,...,-...
9
votes
2answers
904 views

Peculiar error when solving the Poisson equation on a non-uniform mesh (1D only) finite volume method

I have been trying to debug this error the last few days I wondered if anybody has advice on how to proceed. I am solving the Poisson equation for a step charge distribution (a common problem in ...
9
votes
5answers
1k views

Is discontinuous Galerkin really any more parallelizable than continuous Galerkin?

I've always heard that easy parallelization was one of the advantages of DG methods, but I don't really see why any of those reasons don't also apply to continuous Galerkin.
8
votes
1answer
461 views

Finite element convergence rates for mixed problems

I've coded up a Stokes Flow problem using finite elements and am in the process of verifying that it works. I'm just not sure what convergence rate I should be expecting as I globally refine the mesh. ...
8
votes
2answers
319 views

Why does conjugate gradient work with this nonsymmetric preconditioner?

In this previous thread the following multiplicative way to combine symmetric preconditioners $P_1$ and $P_2$ for the symmetric system $Ax=b$ was suggested: \begin{align} P_\text{combo}^{-1} :=& ...
7
votes
1answer
2k views

Stable time step limits for Velocity-Verlet integration

I'm implementing a mass-spring solid mechanics solver and I'd like to use the Velocity-Verlet time integration scheme. However, I cannot find anything about the maximum stable time step -- either ...
7
votes
3answers
487 views

Mixed Finite Element Method for the Stokes System—Some Implementation Details

I am currently working on my bachelor’s diploma. The research concerns mixed finite element method for the 2D Stokes system $$ - \Delta \boldsymbol u + \nabla p = \boldsymbol f, \quad \boldsymbol x \...
6
votes
2answers
12k views

C++ libraries for Fast Fourier Transform in high precision

I am looking for a C++ library for Fast Fourier Transform (FFT) in high precision (e.g., using high precision real data types similar to mpfr_t in MPFR or ...
6
votes
2answers
550 views

Efficiency of a Dynamic Mesh vs. a Static Mesh for a Propagating Shockwave

I have a low speed flow with a high voltage discharge occurring within it between two spherical electrodes. We have quite a bit of data from the experiment and have performed 0-D modeling of the ...
6
votes
2answers
529 views

Large-scale generalized eigenvalue problem with low rank LHS matrix

Assume that we have generalized eigenvalue problem: $B^HB\textbf{x} = \lambda A\textbf{x}$ where $A$ is an nxn Hermitian sparse matrix (n is very large, so we do not have $A^{-1}$ but can solve ...
6
votes
3answers
1k views

Is lattice Boltzmann suitable for simulation of incompressible Stokes flow?

We have a flow that is dominated by adhesion forces from the substrate and surface tension from the free surface. The material is nearly solid and at rest first, and gets a bit less solid by heating. ...
6
votes
1answer
960 views

Grid mapping from an unstructured triangular mesh to a regular rectangular mesh

I am modeling fracture propagation using a 2-D dynamic unstructured grid. As the fracture propagates over time, the elements move accordingly. For a given time step, I would like to interpolate the ...
6
votes
2answers
206 views

Why naively chopped finite difference matrix works for different ODE boundary conditions

We know finite difference method (FDM) can replace $y''(x)$ as $\frac{1}{h^2}[y(x+h)+y(x-h)-2y(x)]$ or so. One naive way to write down the matrix of the differential operator is like the following, ...
6
votes
2answers
279 views

Krylov subspace iterative methods in floating point arithmetic

Is there any work that considers Krylov subspace iterative methods in floating point arithmetic? I'm especially interested in how rounding errors influence the convergence and the accuracy of the ...
6
votes
2answers
2k views

Numerical Integration with Convergence Factor with SciPy: Problem with Improper Integral

I would like to perform the numerical integration of an integral of the form $$ \int_{-\infty}^\infty e^{i \omega 0+} G(i \omega, \mathbf{v}) d \omega ,$$ or, using the symmetry $G(i\omega)^* = G(-i \...
5
votes
3answers
1k views

Performance optimization or tuning possible for Scalapack Gemm?

I'm comparing the performance of distributed gemm, using Scalapack over OpenBLAS, with threaded gemm, using OpenBLAS. It seems quite hard for me to get scalapack to give better results than ...
5
votes
3answers
2k views

Flow past a cylinder - Projection Method - Boundary Conditions

I plan to write a code that solves the flow past a cylinder and try to see the Von-Karman vortex street. I will solve the 2-D viscous, incompressible Navier-Stokes using the projection method. The ...
5
votes
1answer
4k views

Poisson equation with Neumann boundary conditions

I'm trying to solve the Poisson equation with pure Neumann boundary conditions, $$ \nabla^2\phi = \rho \quad in \quad \Omega\\ \mathbf{\nabla}\phi \cdot \mathbf{n} = 0 \quad on \quad \partial \Omega $$...
5
votes
5answers
345 views

Will MPI continue to be a popular basis writing scalable massively parallel solvers on future many-core CPUs? [duplicate]

Possible Duplicate: What programming paradigms should I be investing in if I want my code to run on petascale machines in the future? Having entered the multi-core era (som already refers to as ...
5
votes
2answers
2k views

Fourier Transform of function in Spherical Harmonics

I have a function $f(r,\theta,\phi)$ which I am expressing in terms of spherical harmonics $$ f(r,\theta,\phi) = \sum_{l=0}^{\infty} \sum_{m=-l}^{l} g_{l,m}(r) d_{l,m}(\theta,\phi) $$ where $d_{l,m}$...
4
votes
1answer
336 views

Meshes in codes that do AMR

In light of this question and some stuff I read online I am wondering if large FE libs (e.g., deal.ii, libmesh etc.) that do AMR keep the entire mesh or possibly a coarse version of the entire mesh on ...
4
votes
1answer
121 views

Which optimization method can be used to do the following?

I've the following system of equations for studying information flow in the below graph, $$ \frac{d \phi}{dt} = -M^TDM\phi + \text{noise effects} \hspace{1cm} (1)$$ Here, M is the incidence ...
4
votes
1answer
3k views

Meaning of CFL condition on parabolic problems

I've been studying this FEM theory and for the parabolic problems, there's the analysis of stability of the $\theta$-method. I followed the analysis and they get this CFL (Courant-Friedrich-Lewy) ...
4
votes
2answers
2k views

Optimization with matrix determinant as constraint

I'm solving a constrained optimization for matrix $\mathbf{A}$ with dimension 6x6, where one of the constraints is $\mathrm{det}(\mathbf{A})>0$. I use the NLopt package to solve my problem and ...
4
votes
1answer
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 ...
3
votes
2answers
309 views

Runge Kutta and Milstein – system of second-order coupled differential equations with noise

I would like to solve a system of second-order differential equations to describe the dynamics of a system of particles. Two Newton-like forces are responsible for the motion of each particle $i$: A ...
3
votes
1answer
2k views

Iteratively solving 3D Poisson equation in MATLAB

I have written a function that sets up a sparse matrix A and RHS b for the 3D Poisson equation in a relatively efficient way. The set-up is nothing fancy: I have extended the 2D 5-point stencil to an ...

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