# All Questions

7,522 questions
102 views

### Is there any open-source code for a hybrid 2D mesh (triangles and quadrilaterals)?

The question is pretty much the title. Note that I have lots of experience using open-source meshing tool, e.g. Gmsh and OpenFoam blockMesh & snappyHexMesh. Nevertheless, I have no idea on how to ...
54 views

### Where does the seemingly official number of certain algorithms come from?

There are a lot of algorithms which seem to have been supplied an official number, such as Algorithm 76, Hierarchical clustering using the minimum spanning tree. Another example is Algorithm 123, ...
15 views

### Finite Group (Non-)Isomorphism

I am poking at reproducing some fundamental research in group-theory. In particular, I want to reproduce the OEIS sequence #1. The crux of the problem is not generating potential groups, this can be ...
76 views

### Solving advection equation - periodic conditions - using roll python function [closed]

The original post was on stackoverflow : I transfert it here. I have to solve numerically the advection equation with periodic boundaries conditions : u(t,0) = u(t,L) with L the length of system to ...
71 views

### How to find the nearest/a near positive definite from a given matrix?

I'm given a matrix. How do I find the nearest (or a near) positive definite from it? The matrix can have complex eigenvalues, not be symmetric, etc. However, all its entries are real valued. The ...
43 views

### Finite element convergence rate and possion's ratio

I am running simulations of a cantilever beam where it is fixed on one end and negative force applied to the other end. The first simulation is with 4-node linear quadrilateral elements and the other ...
60 views

### 2d wave equation with finite differences blowing up

I am (naively) trying to solve the 2d wave equation with finite differences. But the system blows up instantly. For simplicity I set the constant $c=1$, then I am left with $$\Delta u =u_{tt}.$$ I ...
61 views

### Are there known accuracy issues between 2D axisymmetric and 3D solutions?

In my full 3D solutions I am solving for the potential throughout a $100\times 200\times 200$ grid. Inside is a ring electrode set to -5V via a Dirichlet boundary condition, and surrounded on all ...
75 views

### 1+x not backwards stable?

If you compute 1+x for x less than the machine precision, the answer will be 1 which is the ...
39 views

### Strain from FEM simulations to strain gauge measurements

I am looking for some intuition in making comparisons of FEM simulations to experimental measurements. In particular, I am interested in comparisons to strain gauge readings, and perhaps even LVDTs. ...
55 views

### tea bag flavors mixing algorithm [closed]

I bought three boxes of tea bags with different flavors (A, B, C). I wish to mix them in such a way that - there is never two consecutive bags of the same flavor (ABCCAB is avoided) ; - the mixing ...
36 views

### Improve optimization speed for a set of similar problems: Quadratic programming with a warm start

I am repeatedly solving quadratic program, $x^T Q x$ with time dependent linear constraints $Ax=b_t$. Dimension of $x$ is around 10000 and there are around 50 constraints. I want to solve the ...
56 views

### Improving convergence of Jacobi iteration to Schur form

I'm using SIMD processor arrays to compute the eigen-decomposition for large numbers of small (up to $32\times 32$) matrices. For assorted technical reasons, Jacobi iteration maps well to the SIMD ...
81 views

### Impose Neumann Boundary Condition in advection-diffusion equation 1D

when solving the advection equation in 1D that is: $$\frac{\partial u}{\partial t} + c\frac{\partial u}{\partial x} = 0$$ with $u'(t,0) = 0$ and $u(t,L) = 0$ , $u(0,x) = u_{0}$ one numerical ...
51 views

### Writing parallel code for molecular computation [duplicate]

I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
66 views

### Condition number of matrix and effects of round off errors

In my numerical linear algebra class, I learned that for some matrices, it could have an element that is a very small number that is approximately 0 (and many orders of magnitude different from all ...
63 views

### Applying neumann boundary conditions to diffusion equation solution in python [duplicate]

For the diffusion equation $$\frac{\partial u(x,t)}{\partial t} = D \frac{\partial ^2 u(x,t)}{\partial x^2} + Cu(x,t)$$ with the boundary conditions $u(-\frac{L}{2},t)=u(\frac{L}{2},t)=0$ I've ...
42 views

### Minimize cost with Levenberg-Marquart method

I want to minimize a cost function of the form, $$\min_{q,t}\left(q^T\left(\mathcal A + \mathcal B\right)q + t^T\mathcal C t+\delta t+\varepsilon Q(q)^TW(q)t+\lambda\left(1-q^Tq\right)^2\right)$$ ...
132 views

### Defining a condition number and termination criteria for Newton's method

The condition number of function evaluation $$\mathrm{cond}(f,x) := \left| \frac{x f'(x)}{f(x)} \right|$$ is infinite at a root of $f$. Hence it is useless for rescaling a tolerance which defines an ...
29 views

### Is it possible to obtain a 'relaxing lengths' for 8 node hexaedral element

I am using 3D FEM with 8-node brick elements to model a certain type of growth/expansion, which is not a plastic deformation. First, I apply a pressure/load and I get displacement and the new position ...
31 views

### Guide for finite-difference schemes for Hamilton-Jacobi-Bellman Equations

I need to solve a simple, low-dimensional Hamilton-Jacobi-Bellman equation. Is there a simple guide for doing this numerically using finite-difference schemes? I found a few research articles ...
79 views

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### Solving multiple linear programs with same constraints but different objective

I have ~30 non-negative variables and 24 equations and I want to find out the upper and lower bound for each variable. Feasible solutions are guaranteed. So for each variable, I solve two LP problem, ...
47 views

### Mass matrix and BDF time integration

I have a system of nonlinear equations on the general form: \begin{align} \mathbf{M}(\bar{y})\dot{\bar{y}} =\bar{f}(\bar{y},t) \end{align} Where $\mathbf{M}(\bar{y})$ is a matrix and $\bar{f}$ is a ...
47 views

### Why do stabilized formulations for the Navier-Stokes equation maintain the convergence rate for high order polynomial interpolation?

I have a quick questions which has been troubling me lately. When reading the FENICS Finite Element Book they assess various approaches to solver the Stokes equation. Obviously, they discuss the ...
49 views

### sum of absolute difference constraint in optimization problem

I am writing a model for an optimization problem. I need to write the following constraint: $$\sum^{N - 1}_i \lvert (a_i - a_{i+1}) \rvert \leq 2\, .$$ How to write this constraint (or linearize)? ...
106 views

### Fast matrix multiplication with matrix elements computed on-the-fly (without forming the matrix)

Is there any library or routine for high-performance matrix-matrix product, where the matrix elements are computed on-the-fly using a given function of $i$ and $j$? More specifically, in the problem ...
75 views

77 views

### Why the MIRACLE of Lanczos/CG-like?

Lanczos/Arnoldi/Rietz/CG-like algorithm share the same core strategy... In each, a little miracle appears, most of the Gram-Schmidt inner products are zeroes! In others words, new direction need only ...
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58 views

### Fast calculation of $A^T B$

I need to compute a matrix-matrix product, $A^T B$, where $A$ is $n \times r$ sparse, and $B$ is $n \times q$ dense. The number of rows $n$ is far larger than both $r$ and $q$. In fact $n$ is so large ...
82 views

### Factorize laplacian in terms of first derivative matrix

I am trying to factorize the following Laplacian matrix in terms of $D^TD$, D is the first derivative matrix. The tridiagonal form of the secon derivative matrix using Neumann boundary condition is ...
34 views

### Numerically solving a system of parabolic PDEs and 1st order ODEs

I'm trying to solve the following system of differential equations numerically. What are the available finite difference approaches and matlab solvers to solve such a system? Other approaches to solve ...
53 views

### Open source distributed sparse-matrix vector multiplication library

What is the current state-of-the-art open source library that has an efficient implementation distributed memory sparse matrix-vector multiplication? I need to perform repeated SpMVs and I am looking ...
22 views

### Semi-Definite relaxation of non-linear constraint?

I am implementing an optimization problem using semi-definite approach. One of my constraints is of following form $trace(A∗X)−(k∗trace(A∗X))+(k∗\sqrt {(trace(B∗X)} )==0$ where k is a constant, A ...
96 views

### Matrix Representation of a Discretization for a Partial Differential Equation

I want to discretize the following problem \begin{cases} \mu \nabla^2u+(\lambda+\mu)\nabla \nabla\cdot u = \rho \frac{\partial^2u }{\partial t^2 } + \beta \frac{\partial u}{\partial t}\\ u(...
20 views

### Why is the method of im2col with GEMM is more efficient than the method of direction implementation with SIMD in CNN

The convolutional layers are most computationally intense parts of Convolutional neural networks (CNNs).Currently the common approach to impement convolutional layers is to expand the image into a ...
106 views

Let's say, I have a compact area $S$ (for example a circle, a square or some arbitrary polygon) and a function $f: S \rightarrow \mathbb{R}$. I want to numerically calculate the Integral $$\int_S f(\... 1answer 75 views ### Multigrid preconditioner for conjugate gradient methods When solving A*x=b using preconditioned conjugate gradient methods one has to solve z=K^{-1}*r for the preconditioning where K is the preconditioner of A and r is the residual vector. ... 1answer 33 views ### Custom exponents for Lennard Jones in LAMMPS I am trying to run an MD simulation using this generalized version of Lennard Jones.$$ U(r) = \left(\frac{r_0}{r}\right)^A -\frac{A}{B}\left( \frac{r_0}{r} \right)^B  However, I do not know how ...
I'm trying to solve $\begin{cases} -u''=f \\ u(0)=0 \\ u(1)= \alpha \end{cases}$ with FEM using reference elements and local coordinates. So we have the global ...