Questions tagged [python]

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

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6
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1answer
260 views

Parallelize Scipy iterative methods for linear equation systems(bicgstab) in Python

I need to solve linear equations system Ax = b, where A is a sparse CSR matrix with size 500 000 x 500 000. I'am using scipy.bicgstab and it takes almost 10min to solve this system on my PC and I need ...
0
votes
1answer
94 views

Why this error occurs in my code for Lax Wendroff?

I want to implement the Lax Wendroff method for a non linear advection equation which is $$\frac{u_{i}^{n+1}-u_{i}^{n}}{t} + \frac{f(u_{i+1}^{n})-f(u_{i-1}^{n}) }{2h} -\frac{t}{2h} \left( F_{i+1/2}^{n}...
-1
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1answer
165 views

Converting for loop from matlab to python

I am converting some MATLAB code in to python and have the encountered the error "ValueError Traceback (most recent call last) in 1 for ig in range(nbas): ---->...
0
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1answer
137 views

System of second order ODEs Runge Kutta 4th order

I have two masses, and two springs which are atattched to a wall on one end. For context I attached the system of equations. How can I add a command to see my analytic solution for my system of ...
1
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1answer
1k views

Understanding why scipy.fft.fft (fast Fourier transform) doesn't work as expected

I write the following fast Fourier transform code into my Python notebook expecting to see a plot wherein there's a spike at $1/2\pi$ since that's the frequency of the sin function, but instead I get ...
0
votes
1answer
115 views

How to insert a(x) function in non homogeneous parabolic pde for implicit method in Python?

I have the following inhomogeneous parabolic initial/boundary value problem: $$u_{t}(t,x) = (1-x^{2})u_{xx}(t,x)+u(t,x),$$ for $t \in [0,1]$ and $x \in [-1,1]$ $$u(0,x) = \sin(\pi x),$$ for $x \in [-...
1
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1answer
82 views

What is wrong in the code for this upwind method?

I want to implement the upwind method in following advection equation problem : $$ u_{t}+2 u_{x} =0 ,$$ for $0\leq t \leq 1,$ $0\leq x \leq 1 $ $$ u(0,x) = u_{0}(x) = \begin{cases} 10^4 (0.1-...
0
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1answer
81 views

create a heavyside function with any value on python

What I'm trying to do is simply a variation of a heavyside function, for 3 before the discontinuity and 4 after. But when I plot it, at the discontinuity it's not a straight vertical line but a sort ...
1
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2answers
266 views

vtk python visualizing scalar data on quad mesh

I'd like to visualize scalar data located on the nodes of a quad mesh (2D) using VTK in Python3. The closest example I've found is vtk quad mesh, but it only seems to visualize the mesh, not data on ...
0
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0answers
55 views

how can I plot specific iterations?

I have made this code for an explicit Euler method but I want to plot only the 0,1,25,50 iterations not all of them.How can I do it? ...
0
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0answers
119 views

Phase portrait of non-linear system of ode (Triple Galaxy System)

Context: Hello, I am an undergrad student of physics self-studying Python Programming. I am trying to find the value of H_lam for which limit cycles corresponding ...
0
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1answer
75 views

How can I deal with optimization problems that have a sum of functions of Z as a constraint when Z is the quantity to be minimized?

I have a problem where I have to minimize a certain quantity $Z$ subject to the following constraints:- $w_1 + w_2 + w_3 = 1$ $\frac{f_1(w_1*Z) + f_2(w_2 * Z) + f_3(w_3 * Z)}{Z} >= k$ where $k$ ...
0
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0answers
146 views

Solving 1D wave equation with finite difference method

I've written a code in Python to solve the 1D wave equation with the finite difference method (the explicit and the implicit methods). I'm trying to perform a mesh convergence study to estimate the ...
1
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1answer
136 views

How can I color my Mandelbrot set like this?

I have a background image of a fractal on my phone that I would like in a higher resolution with super sampling, and decided to write my own program for it. I've got down rendering a Mandelbrot set, ...
2
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1answer
63 views

Python documentation on creation of an exponential random variable [closed]

I didn't really know if this stack was the right place to post but I was reading the documentation for creating an exponential random variable in numpy. But isn't there a typo. Like shouldn't it be : $...
0
votes
1answer
173 views

SciPy odeint fails in unpredictable ways on deterministic system of ODEs

I've been trying to solve the following (relatively simple) system of Lotka-Volterra ODEs in Python using SciPy's odeint: $$\dot{z_1} = z_1 \left(- \sigma z_1 + \sigma z_2 + \rho z_3 - z_4 - z_5\right)...
1
vote
1answer
79 views

Define continuous, non-analytical pdfs in python

I am planning to do some basic algebra on continuous, non-analytical random variabels. I want to define their probability density functions as arrays x and f(x). Yet, I was surprised to find out that ...
3
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2answers
101 views

Compute $tr(A^TBC)$ in Python

I have to compute the trace of the product between three matrices $A,B,C$ in python, i.e. I have to compute $tr(A^TBC)$ and I was wondering what was a good way to do it in Python(here $A^T$ is the ...
0
votes
0answers
62 views

Python evaluating a second order ODE with RK4

Pasted below is my python code. It is a 4th order runge kutta that evaluates the 2nd order ode: y'' +4y'+2y=0 with initial conditions y(0)=1, y'(0)=3. I need help fixing it. When I run my code, my ...
0
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0answers
20 views

3d surface image for given datasets

I have some data that looks like as follows x-cor y-cor z-cor 0.02 0.0251 0.02 0.01 0.0257 0.02 0.014 0.02 0.03 0.023 0.003 0.05 0.013 0.002 0.77 .................... .................... ...
0
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1answer
72 views

Sum of random variables - Check your derived distribution against a numerical calculation/histogram

Consider independent random variates $X_0, X_1, . . .$ each uniformly distributed on the support $[0, 1)$ Let's say $Y = X_0 + X_1$, where $X_0$ and $X_1$ are independent uniform random variables with ...
3
votes
1answer
282 views

Calculating Error for Poisson Equation using Successive Over-Relaxation technique, Python

I am trying to solve the Poisson Equation $\frac{\partial^2 T}{\partial x^2} + \frac{\partial^2 T}{\partial y^2} = 32(x(x-1) + y(y-1))$ for a 61x61 grid using Python3 with boundary conditions being $T=...
2
votes
2answers
373 views

Use Monte Carlo integration to compute the volume and centre of mass in Python

In particular, I want to focus on finding the volume $V$ because I will need it to start working on solving the centre of mass This $3D$ homogenous body (Torus section) is defined by $$x^2 + \left(\...
2
votes
2answers
211 views

(Lack of) Availability of Finite-Difference library for simple 2D PDEs

I would like to solve two types of simple 2D problems, namely the stationary heat equation on an L shaped geometry like this: And also compute the magnetostactic field in an air gap of the following ...
0
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0answers
26 views

Negative binomial expansion of general symbolic polynomial

Using Sympy, I would like to compute the negative binomial expansion of a general symbolic polynomial, e.g., $(x_1 + x_2 + x_3 + 4 x_4)^{-1}$. I understand that I can go by recursively partitioning ...
1
vote
1answer
696 views

Numerical integration problem: IntegrationWarning The integral is probably divergent, or slowly convergent

I am trying to get the numerical integration of a function using scipy's integrate.quad as follows. $$ \begin{equation} G (\alpha) = \frac{4\alpha}{\pi}\int_0^{\...
0
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1answer
104 views

Odeint error for nonlineal differential equations

I receive the following error when I run the code. ODEintWarning: Excess work done on this call (perhaps wrong Dfun type). Run with full_output = 1 to get quantitative information. warnings.warn(...
0
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0answers
27 views

How can I change th code to implement the Fourier series as defined?

I want to compute the Fourier series expansion of the function $$f:[-1,1] \to \mathbb{R}$$ with $$f(x) = \begin{cases} -x & x < 0 \\ 0 & x \geq 0 \end{cases} $$ .The code ...
2
votes
2answers
463 views

Python scipy eigh(Arpack) giving wrong eigenvalues for generalized eigenvalue problem

I am trying to solve a generalized eigenvalue problem using Arpack, right now the code is using LAPACK but that's too slow, we only need a few eigenvalues and the matrices are sparse so using Arpack ...
4
votes
2answers
237 views

Meshing surface of a sphere with a subdomain

I am trying to build a triangle mesh of the surface of a sphere which also includes a subdomain defined by a 'polygon'. Here is a successful example (subdomain defined by the red dots): Note that the ...
16
votes
1answer
3k views

How can I avoid catastrophic cancellation?

I have the following formula that I need to rewrite in order to avoid catastrophic cancellation. $$y =\sqrt{\frac{1}{2}\left(1-\sqrt{1-x^{2}}\right)}$$ As $x$ becomes smaller, $\sqrt{1-x^{2}}$ ...
1
vote
1answer
161 views

FEM does not match exact solution

I am trying to solve : $$-u''(x) + u(x) = \sin(2\pi x)\, ,\quad 0<x<1\, ,$$ $t>0$, with $u(0) = u(1) = 0$. That has as exact solution $$u(x) = \frac{\sin(2\pi x)}{1 + 4\pi^2}\, .$$ But the ...
0
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0answers
290 views

How to take convolution of two arrays in Python by using NumPy?

Generally, we know that if we have this relation between Fourier transforms of three functions in frequency domain as: $$\mathfrak{F}\{\mathsf{P}(t)\} = \mathfrak{F}\{\mathsf{Z}(t)\}\mathfrak{F}\{\...
3
votes
1answer
143 views

How to get a more accurate cancelation

I shall try to get to the point, so let me know if there is something left and you need more details. I am solving a couple of equations that are not coupled explicitly, but their corresponding ...
1
vote
1answer
311 views

DOP853 integration method is missing (SciPy)

I was checking some integration methods provided by SciPy, in which the DOP853 should be included according to the webpage (https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate....
1
vote
1answer
114 views

Coupled second-order differential equations using runge kutta 45

As a little summer project I have tried to make a ballistic calculator for when I play football, (following an example from a book), just to learn some numerical methods while doing so. My problem is ...
1
vote
1answer
44 views

Effecient method for iterating over sparse dataset

Apologies if this isn't the appropriate forum for this question. I have a set of elements that I need to iterate over as part of a modeling workflow. The elements exists over a set of dimensions (i, ...
3
votes
2answers
1k views

Generate random smooth 2D closed curves

I would like to know how can I generate a collection of random 2D closed smooth curves. I thought about generating a random 3D surface with random peaks, and then intersecting the Z=0 plane with it, ...
0
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0answers
28 views

Set of integrators do not consistently solve an equation in Python

I must solve the following second order differential equation: $\delta \phi^{''}_{\mathbf{k}}+(3-\epsilon)\delta \phi^{'}_{\mathbf{k}}+\left(\frac{k^2}{a^2 H^2}+\frac{V_{,\phi\phi}}{H^2}-6\epsilon +4\...
4
votes
1answer
228 views

Imposing no flux boundary conditions on variants of the Cahn-Hilliard equation using Finite Differences in Python

I have been looking into simulations of phase separation in variants of the Cahn-Hilliard system and have been running into issues with implementing no flux boundary conditions on certain variants. ...
1
vote
1answer
70 views

How to optimize nuclear norm subject to positive semidefinite constraints?

For finite dimensional symmetric positive semidefinite matrices $A$ and $B$, I would like to solve \begin{align}&\min |X - A|_1 \\ &\text{subject to}\\ &X \preceq B \\ &0 \preceq X\...
2
votes
1answer
2k views

Solving Lotka-Volterra Equations on Python

I'm trying to plot Lotka-Volterra Equations using Python. I am a real beginner when it comes to Python. I have these two equations: $$\frac{dR}{dt}=\alpha R-\gamma RF$$ and $$\frac{dF}{dt}=-\beta F+\...
2
votes
1answer
136 views

Why is $1/r^2$ force law giving spiral trajectory?

I have written a program to solve for Newton's 2nd Law of motion for a given force law, in 2D polar coordinates. It is known that if the force law is of the form $k/r^2$,we get conic sections as ...
0
votes
1answer
271 views

How to use cumtrapz correctly?

I have tried to do a trapeze integration with f(x)=x^2, where I know how the antiderivative looks like, so F(x) = (1/3)x^3 Here's my code, just like I tried: ...
0
votes
0answers
155 views

Plotting a Magnetic Field in Spherical Coordinates in Python

I am modeling a Helmholtz Coil as two dipoles from far away and I want to plot the magnetic field. $$\mathbf{B}(\mathbf{r}) = \frac{\mu_0 |\mathbf{m}|}{4\pi r^3}\left(2\cos\theta\,\hat{\mathbf{r}} + \...
4
votes
3answers
163 views

I wrote a 2D Finite Element program for Axial Loaded Plates, but the results are unexpected

TLDR: I used Python to write a 2D Finite Element program using 'Constant Strain Triangles' and my beam keeps pointing slightly upwards instead of straight sideways (like the force). I'm new to FEA and ...
0
votes
0answers
123 views

scipy's solve_ivp returns erroneous results for a stiff differential equation

I'm using scipy's solve_ivp for solving a stiff differential equation. I'm using method BDF for solving the same. I have already used MATLAB's ode23s and I'm getting correct results in MATLAB. However,...
0
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0answers
146 views

A parallelized GMRES solver?

My application calls for solving a dense, 40,000 x 40,000, ill-conditioned linear system. The native SciPy GMRES solver with preconditioning has worked well for my application and solving a single ...
3
votes
1answer
46 views

Ising NiO model energy

I am simulating Ising model for NiO. I have simulated for 2d,3d,triangular lattices, and have tried to do the same with NiO model. There are papers which say that the ground state energy is around -...
0
votes
1answer
288 views

Norm constraint in CVXPY

I'm trying to implement the algorithm outlined in https://arxiv.org/abs/1211.5608 on a small scale. I have a linear operator $\mathcal{A}$ which is defined as $$\text{trace}(A^*_l(hm^*))$$ where $$A_l ...

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