Questions tagged [python]

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

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1answer
39 views

How to implement tolerance checking within a for loop whilst performing a numerical integration using a trapezoidal function?

Currently, I have this working code where I have been able to successfully calculate the integration for standard results. But in terms of precision, how could I achieve a good tolerance? ...
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1answer
69 views

Newman algorithm yielding different result to what is given in his paper

Summary I am trying to implement Newman's algorithm for community detection, outlined in this paper. I am testing my implementation against one of the datasets used in that paper to benchmark the ...
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1answer
306 views

Solving an ODE using odeint in Python and continuing the integration

The following relates to the linked question: Scattering of waves in a symmetrical potential (using python) I have attempted to solve the problem for $U(r)$ using ...
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1answer
199 views

How to change the value of a variable at some point lying in the time interval of solver in solve_ivp

The following code solves a differential equation with scipy: ...
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1answer
781 views

How can I evaluate more accurate energy eigenvalues from Schrodinger equation using shooting method?

I am trying to use the "shooting method" for solving Schrodinger's equation for a reasonably arbitrary potential in 1D. But the eigenvalues so evaluated in the case of potentials that do not have hard ...
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1answer
22 views

Python: Getting second output variable from minimizing a computationally intensive function on first outputs

I have a function in python that is quite computationally expensive to evaluate, of the form: ...
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1answer
756 views

solve_ivp - Overflow encountered in double_scalars

I'm modeling an electron that orbits the nucleus. Of course, charged particles radiate away there energy so it'll crash into the nucleus. My approach has been to to evaluate the coulomb force and add ...
2
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1answer
315 views

How to implement Simpson's rule for double integral (without numeric limits of first integral)

I want to use Simpson's rule to evaluate the following double integral: $$\int_{a}^{b}\left|\int_{0}^{z}x\cdot \mathrm{erf}(x-10)\cdot J_{0}(x) \mathrm{dx}\right|^{2}\exp(-0.5*(z-40)^2)\mathrm{dz} $$ ...
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0answers
71 views

Scipy.integrate.odeint is returning curves with almost the same frequency for different damping ratios, shouldn't they be different?

I am trying to solve the ODE for a harmonic oscillator using Scipy's odeint solver for different dampening factors. I'm using the following code, based off of this example: ...
2
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1answer
420 views

Coding of the Legendre polynomial and the infinite sum using python

I'm looking to code the following function: $$|g(\theta)=\frac{1}{2k}\sum_{\ell=0}^{\infty} (2\ell +1)\sin(2\delta_{\ell})P_{\ell}\cos(\theta)|^2$$ ...
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2answers
84 views

Distributed computation with computers around me

I know for large amounts of data there are online computation services or supercomputers or Beowulf cluster. For a small quantity of data, a good computer is enough. But sometimes, for medium qty of ...
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0answers
446 views

Using Spherical Bessel Functions in Python

My question relates to using spherical Bessel functions in Python. If my ODE contains a spherical Bessel function of the form $$j_\ell(tx)$$ and similarly $$y_\ell(tx)$$ for given values of $t$ and $...
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1answer
221 views

Translating the Euler code in scipy's solve_ivp

My code is based on the similarity transformation X=VZ.I simulate the model for transformed equations involving Z by replacing ...
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0answers
582 views

Solving nonlinear pendulum using Runge-Kutta 4 for smaller steps

I am trying to solve nonlinear pendulum using 4th order Runge-Kutta method for limits between a=0.0 to b=110 seconds and simulated the results to observe the pendulum movement. But when I increase the ...
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1answer
334 views

Numerical calculation of Wannier function in optical lattice

I am working out some optical lattice band structures (example here). I have no issue with setting up the eigenvalue equation: $$ H_{jj'}c_{j'}=Ec_{j'} $$ Where $H$ is the tri-diagonal matrix that ...
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1answer
119 views

Best way to convert a sparse (containing zeros) covariance matrix into a correlation matrix?

I have a $100$x$100$ covariance matrix that looks like this. Some rows/cols are all-zero because those corresponding elements are not present in the sample from which covariance is calculated. I'm ...
2
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1answer
983 views

Vectorised second order ode solving in python

I am trying to write a python program that simulates the motion of a large number of particles by numerically integrating a second order ordinary differential equation. I first split the ODE into two ...
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2answers
193 views

Solving a Boundary Value Question $\frac{d^2y}{dx^2}=y\cos(x)+\frac{\sin(x)}{x^2+2}$ using Python

I'm looking to solve this boundary value question using the shooting method! $$\frac{d^2y}{dx^2}=y\cos(x)+\frac{\sin(x)}{x^2+2}$$ given the initial values: $$y'(x=-1)=-1\\y'(x=5)=0$$ I'm aware of ...
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1answer
217 views

Double Integral with Gauss- Hermite for one component

I am trying to perform the following integral $$\int_{0}^{2\pi}\int_{0}^{+\infty} \frac{r'\left(e^{-r'^2/2\sigma^2}\right)\left(r-r'\cos(\theta-\theta')\right)}{r^2+r'^2-2rr'\cos(\theta-\theta')}dr'...
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1answer
220 views

Plot of a function involving an integral and value changing parameters [closed]

I'm trying to plot the cross section with respect to the photon energy $h\nu$ but for $\gamma = 1.0, 1.2, 2.0 $ in the same axes $\sigma = \left[\left(\frac{\xi_{eff}}{\xi_{0}}\right)^2 \frac{n_r}{\...
3
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1answer
586 views

Setting up optimization problem in GEKKO

I have the following dynamical system, $\frac{d \phi}{dt} = -M^TDM\phi \tag{1}\label{1}$ $\frac{d \hat\phi}{dt} = -M^T\tilde{D}M\hat \phi \tag{2} \label{2}$ $\eqref{1}$ represents the exact ...
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2answers
357 views

Convolution in Python

I have an integral of a convolution between two functions. How can I calculate this in Python? It is a continuum convolution.
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1answer
154 views

Numpys `tensordot` and what is happening mathematically

I've encountered a program where np.tensordot was used, so I tried looking it up but I can't really understand what this function is doing... I feel rather ...
7
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1answer
173 views

Numerically stable and fast sum of last K elements in sequence

Suppose I have a long, possibly infinite, sequence $x := [x_1, x_2, ...]$, and I want to use it to compute another sequence $y:=[y_1, y_2, ...]$ where each element is the sum of the last K elements of ...
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1answer
151 views

Is this behaviour normal for a Lennard-Jones monte carlo simulation?

I am simulating a Lennard-Jones fluid using MC simulation. The code always uses a reduced unit. I want to find the potential energy of the system. Periodic boundary condition implemented. I have ...
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1answer
122 views

How to get free energy surface of a 3d Ising Spin system using Monte Carlo simulation?

I am doing a Monte Carlo Simulation of the properties of a 3D Ising Spin system. I want to get the free energy surface of the spin system from the simulation. It is a magnetization vs free energy ...
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0answers
149 views

2D diffusion equation using Finite Volume Method

i am working on an assignment problem: Consider a two-dimensional rectangular plate of dimension L = 1 m in the x direction and H = 2 m in the y direction. The plate material has constant thermal ...
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1answer
218 views

Why the magnetisation shows abrupt behaviour for this 3D ising spin system

I am trying to simulate a 3D Ising spin system (+1 & -1) using Monte Carlo Metropolis Algorithm. I want to get different physical quantities from this simulation like magnetization, Average Energy,...
2
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0answers
76 views

Lexicographically order matrix into a vector

I am trying to implement the algorithm contained in this article here. It is about solving a 2 and 2.5D Fredholm integral, focused on bidimensional NMR experiments. I've made significant progress, ...
4
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1answer
317 views

Absence of Discontinuity in Specific Heat Plot Simulated by Ising Model

I am working on 2D Ising model, when I plot "specific heat vs temperature", I can't see any discontinuity at critical temperature around Tc ~ 2.7K. I am enclosing results of all other thermodynamic ...
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1answer
304 views

Solving a large system of coupled ode. (Python)

I really have a problem here. I have not found a solution yet. The system I need to solve similar to this:(Basic idea) $$c_1 = \dfrac{dx}{dr}+y$$ $$c_2 = \dfrac{dy}{dr}+x$$ Both $c_1/ c_2$ are ...
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1answer
1k views

Simple Harmonic Motion using the leapfrog method

I have to use the leapfrog method to solve the simple harmonic oscillator and I having trouble writing it in code. This is what we were given in class $$ \frac{v_{n+1/2}-v_{n-1/2}}{\Delta t}=-\omega_0^...
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1answer
104 views

If not MATLAB, what software/programming language should I use to simulate/animate wave functions in various potentials + more? (example given)

I want to integrate programming into my learning in math and science in a very specific way. I want to create visualizations and simulations of concepts I am learning. When I learn a numerical method ...
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0answers
293 views

Parallel plate capacitor as simple superposition of Coulomb-fields

I am trying to calculate and visualize the electric field inside and outside of a parallel plate capacitor by assuming a uniform distribution of point charges on each plate and by adding up the ...
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2answers
225 views

Arbitrary Precision Optimization Libraries?

Are there any well-known optimization libraries (ideally with Python bindings or even in Python) supporting (unconstrained) minimization (of $f:\mathbb{R}^n \to \mathbb{R}$ for $n$ for $n\sim 10^1,10^...
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0answers
32 views

SHREC 2010 Descriptors

I will appreciate if I may find someone how can clarify for me the part regarding the quality of feature descriptor, shown in the figure below: and this screenshot is from the article: SHREC All my ...
4
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2answers
464 views

Fastest Way to Mutiply $10^4$ 2x2 Matrices

In a code that I work with (written in python, but also tagging as matlab because numpy is so close and I could use it if need be), we use a transfer matrix method to compute the properties of a ...
3
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2answers
283 views

Solving ODE with "Jumpy" Coefficients

I'm numerically solving a linear coupled ODE of the form $$y^{\prime}(t) = \hat{M}(t)y(t)=\left[\begin{array}{cc}0& A(t)\\ B(t)& 0\end{array}\right]y(t),$$ and the difficulty I'm running into ...
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0answers
33 views

sequence\ flow analysis with score- beginner data scientist

I'm trying to create a model that will give me the best parts that lead to a maximized score out of a sequence. my data(spark rdd) looks like this: ("dan", "john", "john", "guy", 45) ("john", "dan",...
3
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1answer
169 views

Evaluate 3D Shape Descriptor

I'm trying to create my own 3d shape descriptor, the idea is that how I may evaluate how much my descriptor is well and good? What I checked is that they evaluate descriptors through shape matching, ...
6
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2answers
8k views

Solving coupled differential equations in Python, 2nd order

I have a system of coupled differential equations, one of which is second-order. I am looking for a way to solve them in Python. I would be extremely grateful for any advice on how can I do that! $k$...
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1answer
54 views

How do I graph this in python? [closed]

$$ y=\cases{-\sqrt{|x|}, \quad x\le0\\\sqrt{x}, \quad x>0} $$ I've tried graphing this in python, but can't seem to figure it out. Does anyone know how to do this by chance?
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0answers
161 views

How to minimize a integral function using a constant step gradient method in Python?

I am developing a practical work of the following system of ode \begin{align}x'(t) &= k_1h(t) - (k_2+k_3)x(t)\\ y'(t) &= k_3x(t)\end{align} and $z(t) = (1-k_4)(x(t)+y(t))+k_4h(t)$, where $h(...
4
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1answer
3k views

Efficient ways to numerically evaluate matrix exponentials

What are some computationally efficient ways to solve matrix exponentials, i.e. functions of the form : $f(X)=e^{X}$, where $X$ is a square matrix? So far I have been able to diagonalise some ...
3
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1answer
956 views

Calculation of Mean Square Displacement for Brownian dynamics system with Lennard Jones interactions in python3

I have a problem getting a sensible result for the Mean Square Displacement (MSD) for a simulation of $N$ particles under Brownian dynamics with Lennard-Jones interaction between them with or without ...
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3answers
5k views

How much more work is it to code math models in Python, compared to working with Matlab?

If one had to code up a new dynamical system for a research group at a university, and the university has a Matlab total headcount license so that one could code in Matlab, are there any benefits to ...
2
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2answers
882 views

Implementing Gelfand’s formula for the spectral radius in Python - lack of convergence

For context: Gelfand's formula for the spectral radius is $\lim_{k\rightarrow \infty}|A^k|^{1/k}$ where $|\cdot|$ is any well-defined operator norm. I naively coded a function to calculate the $k$th ...
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0answers
1k views

Numerically solving a partial differential equation in python with Runge Kutta 4

I'm supposed to solve the following partial differential equation in python using Runge-Kutta 4 method in time. $$ \frac{\partial}{\partial t}v(y,t)=Lv(t,y) $$ where $L$ is the following linear ...
2
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1answer
1k views

Numerical Solution to Rayleigh Plesset Equation in Python

I have been trying to numerically solve the Rayleigh-Plesset equation for a sonoluminescence bubble in Python. You can read about this phenomenon here: https://iopscience.iop.org/article/10.1088/0143-...
5
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1answer
113 views

How do I globally change the precision of a piece of code in Python to debug it?

I am solving a system of non-linear equations using the Newton-Raphson method in Python. This involves using the solve(Ax,b) function (...

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