Questions tagged [python]

A general purpose high-level programming language that emphasizes ease of code syntax and readability.

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1answer
40 views

Convex optimization with constraints involving matrix inverse

I have the following convex optimization problem. I would like to ask is there any efficient way to solve it in Python? Can I use CVXOPT package? If so, any detailed instruction? Thanks a lot. $$ \...
3
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2answers
21 views

MINLP with GEKKO - Modeling discrete variables

I'm trying to define a MINLP optimization problem with GEKKO in Python, and I want to use some variables with fixed values. For my first variable, x1, I need to define the following values (as would ...
2
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0answers
47 views

Heisenberg Model python : Specific heat capacity for spin 2

I have the correct plot for specific heat capacity when I am using the formula which is $C_V$ = differentiation of entropy with respect to temperature. However, When I try to calculate $C_V$, by using ...
1
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1answer
37 views

Doing computations on a very large numpy array: streaming the calculation vs out-of-core memory

I am trying to perform a calculation in numpy that depends on several parameters, and involved the creation of many intermediate arrays. These intermediate steps involve integrals over more parameters....
1
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0answers
60 views

How to translate Python infinitely big integer into Cython?

I want to factorize very huge numbers (e.g. 100-bits, 200-bits numbers) with Cython. Hi everyone, I implemented the Elliptic Curve Method for factorization into Python 3.6. Now, I want to speed up my ...
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0answers
35 views

Can I use matplotlib to plot the surface of a 3D body?

If Matplotlib could volume render, I would not ask this question. But it can't. Can I however instead use Matplotlib to plot the surface of a 3D body? I.e. is there a way to (i) triangulate the ...
1
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1answer
77 views

Problem concerning a part of a simulation for the Ising Model

I was wondering if anyone could help me with a simulation in Python (there is a small part of the code where I have a question) about the Ising model. First, I wanted to get the magnetization $M$ ...
-1
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0answers
27 views

Particle in a 2D box

I am trying to compute the wavefunctions of a particle in a 2D box and a 2D harmonic oscillator using Python and then plot them. I was able to do this for the 1D case using ...
1
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1answer
50 views

What is a good library in Python for correlated fits in both the $x$ and $y$ data?

I have $x$ and $y$ data, both of which have their own covariance matrices. scipy.optimize.curve_fit will accept a covariance matrix for the $y$ data, called ...
1
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1answer
54 views

Preconditionning for solving a non-linear system of equations with least squares

I am trying to solve a large system of non-linear equations (about a few hundred equations and variable but with less variable than equations). Given that the system is really sparse and large I am ...
0
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0answers
46 views

Simulate friction arround steady-state point

When simulating a friction dynamic system, I have come to a problem when approaching steady-state. In the example below, a box moves along a surface with a certain friction coefficient: ...
2
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1answer
52 views

Getting Extremal Rays of Cone

So I have a set of linear homogeneous equations $A\vec{x}=0$. I would like to solve this for non-negative solutions. I can solve the system in general and I get the two vectors that span the solution ...
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0answers
15 views

Find all recurring subgraphs/patterns of maximal size in a single undirected, labeled, connected graph

I would like to identify all subgraphs of maximal size (maximum number of nodes) that are recurrent in a single undirected, labeled, connected graph. I provide exemples of input and expected output ...
2
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0answers
43 views

Efficient algorithm to determine the intersection volume of simple convex polyhedra

TLDR: Is there an efficient algorithm to compute the intersection of polyhedra with 8 or fewer vertices? I have two sets of FEM meshes for one geometry (one exhibiting a skin effect). I have to ...
3
votes
1answer
52 views

Get the roots of a Hermite interpolating polynomial

I am using Python 3.7 to write a program that requires me to calculate the root of the Hermite interpolating polynomial, given two points $\epsilon_0$, $\epsilon_1$, the function ($d(\epsilon_0)$,$d(\...
1
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0answers
71 views

How to perform local sensitivity analysis for partial differential equations

I am looking for a way to do local sensitivity analysis for PDEs, preferably in Python. I get the impression that discretizing the equation then treating it as an ODE could work; however, would that ...
1
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1answer
30 views

Draw contour line to represent multiple contours

I have 5 data sets, each includes multiple scatter points. If I use the geom_path function in R, I could obtain 5 contours like the following graph shows. Those five contours are annotated outlines ...
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0answers
46 views

How to get the derivatives of the determinant and inverse of 2nd-order tensor wrt itself in SymPy?

I have a second-order tensor for which I need to compute the derivatives of its determinant and inverse w.r.t. itself. The equations are as follows: $$\frac{\partial \, det(\mathbf{F})}{\partial F_{...
3
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1answer
63 views

Whitening transformation does NOT return a unit covariance matrix

For this question, I am using the following Wiki definition of Matrix whitening: Suppose $X$ is a random (column) vector with non-singular covariance matrix $\Sigma$ and mean 0. Then the ...
1
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0answers
68 views

Solved : Damped spring-mass system, wrong position, correct speed and acceleration

I am modulating a spring-mass system with gravitation and aero drag, with python programming. The spring is hanging vertically and attached a weight. The user then selects a length to drag it down ...
5
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2answers
155 views

Numerical evaluation of a Gaussian Integral in Python?

Goal I'm trying to write code to compute the normalized Gaussian in the following, $$ \begin{equation} \int_{-\infty}^{\infty} \frac{1}{ \sigma \sqrt{2 \pi}} \exp\bigg( - \frac{(x - \mu)^{2}}{2 \...
1
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0answers
58 views

How to use Wolfe-Powell step-size control in quasi-Newton method?

I'm trying to find the minimum of a function using the quasi-Newton method with the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. But I want to change the following implementation, so that: 1) ...
5
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2answers
349 views

Python: vectorizing a structured linear system solve

Overview I am looking for a way to solve a structured linear system in Python without using a for loop (preferably using vectorization, if possible). Background Consider the following linear system:...
1
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1answer
38 views

Interpolating the gradient of a cylindrically symmetric potential field that's 'supposed to' obey the Laplace equation?

The script below tries to implement a Jacobi iterative relaxation of a potential field for an electrostatic lens. It's hot-off-the-press and I've just started to debug and look for things to test it ...
3
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1answer
82 views

Plug-and-go Clebsch-Gordan computation in python?

I started a little project in python, under the assumption that it would be easy to find a routine for numerically computing Clebsch-Gordan coefficients in some library such as scipy. When it came ...
2
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1answer
62 views

How to check experimental data against a theoretical curve? (Python)

I am trying to check the agreement of a dataset against a theoretical curve, specifically a bandstop filter in an RLC circuit. I have generated a function which describes the curve we expect from the ...
2
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1answer
218 views

Forward and backward integration — cause of errors

I write a test program to integrate foward on $[0,T_f]$ and then backward on $[T_f,0]$ from the endpoint of the forward integration an Hamiltonian system: $$ \dot q(t) = \frac{\partial H}{\partial p}(...
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0answers
43 views

Finite dimensional optimization problem over dynamical system

I am interested in solving numerically the following mathematical problem Consider an ode of the form $$ \dot q(t) = f(q(t),t_1,\ldots, t_N),\qquad t\in [0,T], $$ where $q\in \mathbb{R}^n$ is the ...
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0answers
60 views

How reproducible are conda environments?

I am aiming at keeping my scientific studies and analyses reproducible: I am automating them as much as possible, I am sharing them, and I sharing them together with the execution environment(s) I've ...
0
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1answer
42 views

Plotting ratings matrix

Hello fellows and folks. I have been looking to do this for 1 month and still cannot find the way to do it. Here’s what’s going on: I have a csv file called ratings.csv with the following ...
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0answers
47 views

Numerically Approximating the Jacobian and Comparing the Eigenvalues With Analytical Form

I am trying to study the stability of numerical discretization schemes using the Jacobian matrix of the residues with respect to the vector of conserved variables. For a simple diffusion equation ...
1
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2answers
123 views

How to use MeshFunction in FEniCS (dolfin)?

I'm a beginner user of FEniCS and still struggling with some of the basics. Specifically, I have some issues doing the tutorials in the Langtangen-Logg book Solving PDEs in Python - The FEniCS ...
2
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1answer
79 views

How to add extra constraints to a linear system for probabilities?

Background: I have an equation which looks like as follows: $W \times P = R$ $$\left[\begin{array} &{1}&{0}&{0}&-\frac{w_{1}}{w_{o1}} &\dots &{0} &-\frac{w_{1}}{w_{0} } \...
0
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1answer
40 views

Animation using matplotlib

I am trying to animate a plot of two distinct points (blue and green points) moving about the complex unit circle using Python's Matplotlib library. The problem I am having is that the animation does ...
0
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0answers
50 views

Augmented Lagrangian Techniques Frank-Wolfe Algorithm [python]

I'm trying to solve the convex quadratic problem (quadratic min cost flow problem) using the Frank-Wolfe algorithm. $$ \min\{x^TQx+qx: Ex=b,\quad 0\leq x \leq u\} $$ The standard algorithm is okay ...
0
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0answers
68 views

Writing python program for Weierstrass function with Monte Carlo

Our assignment asks us to create a python program to plot the Weierstrass function: Weierstrass function is an example of a pathological real-valued function on the real line. The function has the ...
3
votes
1answer
54 views

Poisson image blending artifacts

I am trying to implement Poisson image blending as in the paper Poisson Image Editing. This is the task of filling in a masked region of an image by minimizing $$\min_f\int_\Omega \left | \nabla f - \...
-1
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1answer
55 views

Simulating magnetic particles in a field free point generated by two opposing magnets

This is probably a long shot with such a short time, but I've been trying to get theoretical data for a project I'm working on. The project involves using a very simplified version of magnetic ...
1
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0answers
29 views

Why does the correlation function of this stochastic differential equation starts at different points?

I am working with the following differential equation: The equation is $$x=\beta +\sqrt{2D} \xi(t)$$ where $\xi(t)$ is a white noise term, with a reflecting wall boundary conditions. After solving ...
0
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1answer
31 views

Specifying mesh spacing for DFT in numpy

I was testing the .fft package of numpy 1.16.1 in Python 3.7.2. In particular I was trying to verify that the transform resembles the analytical one for: $$f(x) = \mathrm{exp}\left[-\left(\frac{x-5}{2}...
1
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1answer
69 views

FFT solver for the Poisson problem with Dirichlet boundary conditions

I am trying to solve the Poisson problem with Dirichlet boundary condition in 1D: \begin{equation} \begin{array}{rcl} - \mu \Delta u & = & f~in~[0,1], \\ u(0) & = & 0, \\ u(1) & = ...
2
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0answers
133 views

Computing the structure factor from positions and radial distribution function [closed]

I'm currently analysing some spatial point patterns that come from some fluid dynamics simulations and I'm having some difficulty computing the structure factor, $S(\pmb{k})$, from both the positions ...
0
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1answer
122 views

How to efficently plot a finite element mesh solution with matplotlib

I am looking for the most efficient way to plot a mesh using matplotlib given the following information, coordinates of each node, what nodes belong to each element, and the value each node has. Below ...
1
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1answer
39 views

How to obtain and form a 1st order differential equation for leapfrog integration from second order one in this example of coulomb drag

I am currently doing a computational physics homework which asked us to use leapfrog to give the relations between timevelocities and time-distance of these two objects. The full question is as ...
0
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0answers
46 views

Finding second excited state of Schrödinger equation with secant Runge Kutta method

In our assignment, we are required to find the energies of the ground state and the first two excited states of the Schrödinger equation in a harmonic potential: $$V = \frac{50 x^2}{(10^{-11})^2}\, .$...
0
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1answer
31 views

How to improve the efficiency of periodicity detection for long time based lined and gapped datasets

Our data set has $10^4$ data points, but has a long baseline and many gaps. As the histogram shows, the horizontal-axis is time and most of the time, there are no data. The vertical-axis is data ...
0
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0answers
59 views

Need help applying Implicit Eulers Method together with Newtons Method on Burgers' Equation

From the inviscid Burgers' equation: $\frac{\partial u}{\partial t}+u\frac{\partial u}{\partial x} = 0$, I get the discretization $\frac{u_i^{n+1}-u_i^n}{\Delta t}+\frac{(u_i^{n+1})^2-(u_{i-1}^n)^2}{\...
3
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4answers
174 views

Numerical integration in Python with unknown constant

I’d like to solve the below equation for the unknown $T$: $$\int_0^\infty \frac{x^2}{\exp\left(\frac{x}{T}\right)-1}\kappa_x \mathrm{d}x = C,$$ where $C$ is a known constant and $\kappa_x$ is some ...
1
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1answer
115 views

Solving differential equation in Python with variable coefficients (I just know the coefficients numerically)

I am trying to implement a routine to solve a differential equation in Python. Basically the kind of equation that I am interested in solving is of the form: $\displaystyle \frac{d}{dx^2} \left(x y(x)...
1
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1answer
61 views

Is there a better way to do run time analysis than this?

I currently have 2 different functions with options to vectorise them: acc_rej_sine(max_iter, algorithm=None) and ...