All Questions

3
votes
1answer
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 ...
2
votes
0answers
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, ...
0
votes
0answers
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 ...
0
votes
1answer
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 ...
2
votes
1answer
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 ...
-1
votes
1answer
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 ...
2
votes
0answers
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 ...
2
votes
0answers
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 ...
3
votes
2answers
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 ...
1
vote
1answer
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. ...
0
votes
1answer
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 ...
3
votes
1answer
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 ...
4
votes
0answers
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 ...
0
votes
1answer
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 ...
0
votes
1answer
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 ...
3
votes
1answer
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 ...
0
votes
1answer
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 ...
0
votes
1answer
42 views

Minimize cost with Levenberg-Marquart method

I want to minimize a cost function of the form, $$ \min_{q,t}\left(q^T\left(\mathcal A + \mathcal B\right)q + t^T\mathcal C t+\delta t+\varepsilon Q(q)^TW(q)t+\lambda\left(1-q^Tq\right)^2\right) $$ ...
6
votes
1answer
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 ...
1
vote
0answers
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 ...
3
votes
0answers
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 ...
1
vote
1answer
79 views

Grid dependence of a numerical model

Statement of the problem Suppose, we consider the following model $$ \begin{array}{l} (1)~\mathbf{u}_t + \mathbf{F(u)}_x = \mathbf{S}(\mathbf{u},\mathbf{w}), \\ (2)~\mathbf{w}_x = \mathbf{P}(\mathbf{...
0
votes
1answer
56 views

How to derive the optimal bayesian solution to a model of two normal distributed populations

In the "Introduction" section of the paper Support-Vector Networks, it mentioned Fisher's solution to a model of two normal distributed populations: My questions are: How to derive equation (1)? I ...
2
votes
0answers
78 views

A Bound for the inverse of the sum of identity and triangular matrix

I wonder if there are any theorems which can help me to calculate an upper bound for the spectral norm of: $$\left\| \left[ I + \sum_{i=1}^{\overline{n}\in\mathbb{N}} \big( C_i - I\big)\right]^{-1}\...
3
votes
0answers
50 views

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, ...
5
votes
1answer
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 ...
2
votes
0answers
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 ...
1
vote
1answer
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)? ...
4
votes
1answer
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 ...
1
vote
1answer
75 views

Shooting method implementation

I have a trouble of defining a Jacobian matrix for my problem. Basically, I have 4 differential equations to be solved. $$ \begin{aligned} \dot x_1(t)&=x_2(t)\\ \dot x_2(t)&=p_2(t)−\sqrt 2 ...
3
votes
2answers
134 views

Asymptotic error of forward Euler

I'm trying to understand the asymptotic error behaviour of forward Euler (finite difference method), as timesteps are decreased (refined), so I feel trust in the method of manufactured solutions (MMS)....
3
votes
0answers
28 views

Minimum axis aliged bounding box of convex polytope

I need to compute a $n-$dimensional integral with $n<10$ on a convex polytope. Since most numerical integration libraries (e.g. Cuba) expect the function to be integrated defined inside an axis ...
1
vote
0answers
83 views

Smallest circumscribed circle in spherical geometry

I work in Python 3 on astrophysics projects. I need to compute the smallest circumscribed circle of a set of points in the sky (so described by Right Ascension and Declination). I have found a code ...
1
vote
0answers
80 views

Lower bound for bilinear form in FEM

I'm searching for lower bounds of bilinear forms arising in FEM for elliptic second order PDEs with mixed boundaries. I did some research and found: $$\max_{v_{h}\in\mathcal{V}_h(\mathcal{\Omega})}a(...
3
votes
0answers
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 ...
3
votes
1answer
154 views

Computational complexity of Newton's method

the classical Newton's method for non-linear systems of equations is $x_{k+1} =x_k-J_F(x_n)^{-1} F(x_n)$. In pratice, rather than compute the inverse of the Jacobian matrix, one solves the systems $...
3
votes
0answers
43 views

Approximate the largest simplex in N-dimensional Delaunay triangulation

I am working on determining the spatial information of a set of $M$ points in $N$-dimensional space. It is well-known that the construction of Delaunay triangulation is expensive in high dimensional ...
0
votes
1answer
35 views

Elliptic PDE: Proving that a 2nd order accurate discretization of the 2nd derivative of the unknown is 2nd order accurate for the unknown itself

For an ODE: $\frac{dy}{dt}=f(y(t),t)$ The Euler Explicit scheme reads: $y_{n+1}=y_{n}+\Delta tf_n$ and it can be easily shown with a Taylor expension that: $y_{n+1}=y_{n}+\Delta t \frac{dy}{dt}|...
1
vote
0answers
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 ...
2
votes
0answers
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 ...
1
vote
0answers
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 ...
0
votes
0answers
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 ...
-1
votes
1answer
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 ...
4
votes
1answer
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(...
1
vote
0answers
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 ...
6
votes
1answer
106 views

How do I integrate a function defined over an arbitrary area?

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(\...
1
vote
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. ...
1
vote
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 ...
0
votes
1answer
26 views

FEM 1D poisson substitution integral issue

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 ...
1
vote
2answers
113 views

Method to find PDE equation coefficient satisfying mean solution?

What is the best approach to go about solving a PDE problem of the type \begin{equation} k^3\Delta u - k(\mathbf{1}\cdot\nabla u) = 0\, ,\\ u=g\; \text{on}\; \Gamma_D\, ,\\ mean(u) = u_\text{...

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