Questions tagged [python]

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

3
votes
1answer
51 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
vote
0answers
65 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 ...
4
votes
2answers
137 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
vote
0answers
39 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
votes
2answers
321 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:...
0
votes
1answer
36 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
votes
1answer
62 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 ...
0
votes
1answer
49 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
votes
1answer
151 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}(...
1
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0answers
39 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 ...
7
votes
0answers
54 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
votes
1answer
41 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 ...
1
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0answers
45 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
vote
2answers
56 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
votes
1answer
67 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
votes
1answer
38 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
votes
0answers
44 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
57 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
36 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
votes
1answer
53 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
vote
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
votes
1answer
27 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
vote
1answer
61 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
votes
0answers
104 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
votes
1answer
69 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
vote
1answer
36 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
votes
0answers
42 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
votes
1answer
30 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
votes
0answers
57 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
votes
4answers
155 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
vote
1answer
108 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
vote
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 ...
0
votes
0answers
25 views

Scipy basinhopping custom step update and constrained looping

I am searching for the global minimum of a certain function and trying to use its gradient (here same as Jacobin) to guide the step counter. However, my x is fix ...
1
vote
2answers
85 views

How to compute 16 different simulations on parallel with pbs script on the same machine

I have a 32 cores machine, and I need to run 16 different dynamics simulations in parallel on it. I want the 16 jobs to run in parallel, not sequentially, on the same machine. The 16 dynamics input ...
0
votes
0answers
22 views

convex atomic function reformulation to meet concave dcp rule requirements

I have an atomic constraint of the form abs(w - w_prev) >= some_threshold It is supposed to get every value equal to or above my threshold. I am working on a ...
0
votes
1answer
59 views

Creating an Interpolation of a w = f(x,y,z) function

I am trying to finish a series of interpolation functions. The problem is more related with organizing the data than how to do the interpolations. Using the RegularGridInterpolator, I created this ...
0
votes
1answer
38 views

Problems with python's interp 2D

I am writing some functions to interpolate data. While using interp2D, somehow, a sample matrix works but when I change the size of the matrix, it returns an error. ...
1
vote
0answers
27 views

Paring Large Numbers Question [closed]

I am writing some simple code to raise a base value to a power then perform some operations on the output. I have included the code I am using now, below ( see end of this message ), also see ...
0
votes
1answer
61 views

Solve multi-dimensional optimization problem using basinhopping

I am searching for an optimization solution, which is a 8d vector representing 4 complex elements, where each element is within the complex circle with maximal radius 1.2. The objective function is: ...
0
votes
1answer
70 views

Python sequence cluster exercise

I am working through an exercise in my textbook and implementing the code in Python to practice dynamic programming. I feel like I am right on the edge of figuring it out, but after many hours, I come ...
0
votes
0answers
15 views

How to choose metrics for evaluating classification results?

Recently we have developed a python library named PyCM specialized for analyzing multi-class confusion matrices. A parameter recommender system has been added in version 1.9 of this module in order ...
2
votes
1answer
57 views

Incorporating a potential barrier in a wave-packet simulation (Fourier Transform method)

I'm trying to simulate the scattering of a wave-packet at a potential barrier in Python. I'm using a Fourier Transform method (not sure if its the same as the Split-Step method), where I apply Fourier ...
2
votes
3answers
134 views

Find a solution of large system of inequalities

I have a large system of homogenous inequalities involving 33 real unknowns of the form $$ \vec{F}(z_i)^T \cdot \vec{X}>0\, $$ where $\vec{X} = \left(x_1,...,x_{24}\right)^T$ are the unknowns and ...
0
votes
1answer
73 views

Combining multiple coupled 1st order equations in python

I'm having serious troubles with solving translating 3 coupled differential equations into python. The 3 DE's stem from a 4th order DE used to calculate the bending moment of an underwater pipeline ...
1
vote
1answer
40 views

Minimizing the used memory in diffusion simulation using Python

I am recently dealing with a diffusion simulation project and I have come up with the following code: ...
0
votes
1answer
77 views

Unexpected solutions solving an ODE using odeint

I am trying to solve a system of 8 coupled differential equations using scipy's odeint. I have already written my code and it runs fine, but the solutions I get are completely different from what I ...
1
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0answers
78 views

SDE solver in python: manual determination of integrator step size (dt)

Aim: I am trying to solve a system of SDEs, while using the SDEint package in python 3.x. It is a system of SDEs adapted from and inspired by the Zombie Apocalypse ...
2
votes
1answer
97 views

How to choose a python parallelization library?

I want to preprocess a relatively large dataset using python. I implemented some Dask parallelization and was stunned by the time reduction. I figure there are other libraries or frameworks I could ...
0
votes
1answer
153 views

Heat diffusion - Is this the correct approach to include Newmann boundary conditions?

Thank you for looking at this problem. Is this the correct approach to include neumann boundary conditions? With this solution temperature is not correct, and there´s no diffusion. The model seems ...
1
vote
0answers
170 views

Speeding up the solution of a large set of nonlinear algebraic equations in `sympy`

I have a quite large algebraic equation system to solve, the system is so large, I can't post the example here, so I am posting it to pastebin. The sympy.solve is ...