Questions tagged [python]

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

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9
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1answer
556 views

How to solve a second order differential equation (diffusion) with boundary conditions using Python

I am having trouble implementing a model from a publication. Huang, K-L.; Holsen, T.M.; Selman, J.R. Ind. Eng. Chem. Res. 2003, 42, 15, 3620–3625 scihub link: https://sci-hub.se/10.1021/ie030109q I ...
0
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2answers
123 views

Implementation of $[X, \cdot]$ as an $n^2 \times n^2$ matrix, where $X$ is an $n \times n$ matrix

Let $M_n(\mathbb{R})$ denote the set of $n\times n$ matrices with real entries. I have an $n\times n$ matrix $X\in M_n(\mathbb{R})$, and I would like to implement the linear operator $[X, \cdot] : M_n(...
3
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1answer
102 views

Parameters estimation with fewer variables than parameters

I am trying to estimate parameters, 4 of them, by fitting a system of 3 ordinary differential equations. I am using a model published that was using 3 parameters and gave a good fit to the data, and I ...
-1
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1answer
5k views

Error in python (jupyter): index 1 is out of bounds for axis 0 with size 1 [closed]

I am an amature in python, I wrote a simple code in jupyter. But it is giving an error. I want to plot a function: ...
3
votes
2answers
183 views

How to solve the integral-like energy equation with Sagdeev potential numerically in Python?

I am trying to numerically solve equation (6) of Lakhina 2021 in Python. The equation is $$\frac{1}{2}\left(\frac{d \phi}{d\xi}\right)^2 + S(\phi, M) = 0\, .$$ The Sagdeev potential expression is ...
2
votes
1answer
1k views

Error in Simpson's 3/8 rule is higher than that of Simpson's 1/3 rule

For a given function $f(x)$, I have tried to find its numerical integral using Simpson's 1/3 and Simpson's 3/8 rules. I then compare the solution from the numerical quadratures to the analytical ...
2
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2answers
180 views

Single hexahedral element stiffness matrix problem, help me find the mistake

Attached below is some code I wrote to solve a basic problem: finding the node displacements of a cube with two vertices constrained (vertices 6 and 7 with coordinates ...
1
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2answers
52 views

scipy odeint: excess work done on this call depending on initial values even with analytically solvable ODE

I am trying to solve a differential equation in the form: dx/dt = funct(x) using scipy odeint. However, for some initial values, I get a "ODEintWarning: Excess work done on this call", even ...
0
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0answers
45 views

Plotting the motion of a positive charge in a cylindrically symmetric magnetic field

I want to plot the motion of a positive charge in a cylindrically symmetric magnetic field. I am assuming a cylinder around the z-axis, with the magnetic field going in clockwise direction. The B-...
12
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1answer
5k views

Meaning of "-0.0" in Python?

We are finding in Python some occasional errors in our coordinate transforms and other similar computations that produce a result of -0.0. What purpose does this ...
2
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0answers
50 views

Adding a "cost term" to a linear regression, so solution values are minimized

I'm using Python's optimize.lsq_linear method to run a linear regression with the bounds set between 0% and 100% power usage. ...
1
vote
1answer
126 views

Efficiency of scipy.sparse.linalg.expm_multiply with sparse vs unsparse vectors

From the package scipy.sparse.linalg in Python, calling expm_multiply(X, v) allows you to compute the vector ...
4
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0answers
59 views

Solving multiple linear regression in parallel

I am working on a problem where I need to solve approximately 500 Million Linear Regressions (OLS). What would be the most efficient way to do this (e.g. using GPU or a some framework that can do this ...
3
votes
3answers
278 views

Convolute a gaussian kernel with a large array of off-grid centroids without looping? (how to make "A Thousand (Gaussian) Points of Light" )

For a finite object size diffraction simulator, I need to generate arrays which are the sum of thousands of instances of a Gaussian (or other) 2D kernel at centroids that will not fall in any ...
1
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1answer
159 views

How to generate the convolution of f(x, y) with a parametric function g(t), x(t), y(t) in Python? (Something better than this brute-force sum)

The answer to Convolute a gaussian kernel with a large array of off-grid centroids without looping? (how to make "A Thousand (Gaussian) Points of Light" ) involves summing a 3D array over ...
1
vote
1answer
99 views

Numerical solution to the infinite well problem

I've used the following code to implement it ...
-1
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1answer
190 views

Using ODE to plot particle-motion with scipy.integrate.solve_ivp

My Problem: A positively charged particle (mass = 2 * 10-27 kg) is moving along the x-axis. It is travelling in a homogenous magnetic field such that the field axis in z-direction. The energy of the ...
0
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0answers
137 views

Do the projection (with Jacobian) and marginalisation (inversion of matrix and remove a row/column and reinversion) commute?

I try to check the equality or the inequality between 2 Fisher matrices. The goal is too see if the projection (with Jacobian) and marginalisation (inversion of matrix and remove a row/column and ...
-1
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1answer
344 views

Fitting using curve_fit of scipy in python gives totally different answer for 1/t and t

I was trying to fit some data to a single degree exponential decay function but a*exp(-x*t) and a*exp(-x/t) gives completely ...
0
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1answer
65 views

Trying to do a 2D random walk for a particle

I am trying to perform a two-dimensional random walk for a particle, but I am not getting the desired result. The plot produced is a linear plot, which obviously should not have been. Similar code for ...
0
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2answers
104 views

Passing in user inputs with mpirun

I am building a quantum circuit simulator using mpi4py. The simulator takes user inputs to build the initial system and quantum gates the system passes through. I can get the code to work if I do not ...
-2
votes
2answers
91 views

numerical solution for differential equation

I have these 3 equations and i want to solve them with numerical methods. so I am using scipy library but I don't know how to solve 3 equations together. R, g, sigma and density are constants. \begin{...
0
votes
0answers
76 views

How to distinguish primary hosts (stars) and orbiting satellites (planets) and tertiary bodies (moons) by their mass and trajectory?

I posted this question in the astronomy stackexchange. There are no responses, and it was suggested that I pose the question here. The "too long, didn't read" was taken from a comment, and ...
-1
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1answer
2k views

Generate 3D "matrix" with Pandas, based on comparing two dataframes [Python]

Good morning everyone. I am working with Python and Pandas. I have two DataFrames, of the following type: ...
0
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0answers
23 views

Why does this Non-Standard FDTD implementation lead to infinite increase in the magnitude of an EM pulse?

I have been working on a Particle-In-Cell Framework in Python and have noticed an issue where the magnitude of a EM pulse increasing infinitely as the simulation updates. Currently, I am using the Non-...
1
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0answers
52 views

Ising model in Python (Magnetization Scaling)

I am trying to implement the Ising Model in Python for Gibbs Distribution: $$\pi(x) = \frac{1}{Z(\beta)} e^{-\beta H(x)}$$ \begin{align*} p(x,y)&=r(x,y) \cdot \min \left( \frac{\pi(y)}{\pi(x)},1 \...
-1
votes
1answer
112 views

In a random walk simulation, how do I get the mean and standard deviation of how many times the walk returns to the origin?

So I'm simulating a 1-dimensional random walk, with 1000 walks that each take 1000 steps. How do I calculate the average number of times that a walker returns to the origin and then the standard ...
2
votes
1answer
277 views

How is the fuzzy logic calculated in scikit-fuzzy?

I am following this example from documentation of scikit-fuzzy library, but cannot figure out the math behind fuzzy rules there. Here is a short version of the ...
0
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0answers
50 views

Vector Form Using the Curl (Line Integral ) in Python

There is an example in Vector Calculus from Madsen & Tromba page 435 that states: Let $F=(xy^2,y+x)$.Integrate $(\nabla \times F)\cdot k$ over the region in the first quadrant bounded by the ...
0
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1answer
43 views

Question about scipy’s ivp solver

there is one thing I don’t understand. Is the tolerance to compute the step size updated at each timestep or fixed at all timestep. Also, when we look at the documentation and how the tolerance is ...
3
votes
1answer
354 views

Solving numerically the 1D Kuramoto-Sivashinsky Equation using spectral methods

Lately, I've been trying to solve numerically the 1D Kuramoto-Sivashinsky Equation using spectral methods. Let $\nu$ be the viscosity and $[0,L]$ the domain. The 1D equation is, $$ u_t + uu_x + u_{xx} ...
2
votes
3answers
190 views

Solving a PDE with 2 variables, with one variable whose derivative with respect to space is only known

I am trying to solve a PDE of the form $$\frac{\partial u}{\partial t} = D \frac{\partial^2u}{\partial x^2} + k\ \ \ (1)$$ where only $k$'s first derivative with respect to $x$ is known $$\frac{\...
2
votes
1answer
113 views

Solving the 2D Rectangular Waveguide PDE with a Neumann boundary condition for TE modes

I am trying to find the possible modes of a 2d rectangular waveguide by solving the equation, $$\Big(\frac{\partial^2}{\partial x^2} + \frac{\partial^2}{\partial y^2} + \gamma^2 \Big)\psi = 0$$ where $...
2
votes
4answers
198 views

Eigenvalue decomposition for a very huge matrix of medical images (such as the pixel physical coordinates of CT images)

I am trying to do eigenvalue decomposition for a huge matrix larger than 788000×788000 for medical image analysis. The matrix is not sparse and every element in the matrix has a real value. And, for ...
0
votes
1answer
199 views

Pseudospectrum of non square Matrix in Python

I have a rectangular matrix $A \in \mathbb{R}^{m \times n}$ ...
3
votes
0answers
28 views

Unexpected CUDA processing time dependency on thread count [closed]

When calling a kernel function, the number of threads per block should ideally be a multiple of the warp size. This yields more efficient use of resources and lower processing times. However, there ...
3
votes
1answer
113 views

Lanczos algorithm for finding top eigenvalues of a matrix sum

I am trying to find the top k leading eigenvalues of a NumPy matrix (using python dot product notation) L@L + a*X@X.T, where $L$ ...
0
votes
0answers
63 views

How to efficiently perform this 2D integral in Quadpy?

I need to integrate a function defined in 2Dims (z and radius r), for which I don't have an expression. I can just query the ...
-1
votes
1answer
46 views

Generating Rvs for a given PDf in python

Two random variables $X$ and $Y$ are distributed according to \begin{align} f_{XY}(x,y)= \begin{cases} x+y & 0\leq x \leq 1, 0\leq y \leq 1 \\ 0 & otherwise \end{cases} \end{align} I ...
0
votes
0answers
202 views

Numerical Range of a matrix in Python

In the mathematical field of linear algebra and convex analysis, the numerical range or field of values of a complex $n\times n$ matrix $A$ is the set $$W(A)=\left\{{\frac {{\mathbf {x}}^{*}A{\...
0
votes
1answer
276 views

Error using scipy.integrate.solve_ivp: index error: the index 0 is out of bounds for axis 0 with size 0

I am recently working on the code based on the stick-slip phenomenon in Python. It's the stick-slip oscillator (chapter 3.4) in https://www.sciencedirect.com/science/article/pii/S0888327020301205. And ...
0
votes
1answer
275 views

N-body problem with differents solvers (RK2, RK4, Euler symplectic, Stormer-Verlet) : planets drift to infinity

I'm trying to write an integrator for the 2 and 3-body problem. I choose to start from a generalisation to N-body problem so I can just pass my bodies to the same integrator in the two cases. I'm ...
0
votes
0answers
51 views

Newton-Raphson for estimating Weibull distribution does not converge

I've been trying to estimate the two-parameter (a,b) Weibull distribution (loc. param. = 0). $$f(t;a,b)=\frac{b}{a}\left(\frac{t}{a}\right)^{b-1}\exp(- \left(\frac{t}{a}\right)^b) $$ To find the ...
2
votes
0answers
127 views

Errors in Integral Estimate of Gaussian using Trapezoidal Rule

I'm trying to estimate the percentage error in computing the integral of a Gaussian via composite trapezoidal rule versus via an exact formula. To do this I've generated a gaussian with mean 0, ...
0
votes
1answer
84 views

High Running Time and Suboptimal Accuracy of 2D Wave Equation Solver with Finite Differences

Im trying to solve the following 2D wave equation: $$u_{tt} = u_{xx} + u_{yy}, \hspace{3mm} u(x,y,0) = \cos(4 \pi x) \sin(4 \pi y), \hspace{3mm} u_t(x,y,0) = 0$$ with the periodic boundary condition ...
1
vote
1answer
42 views

Looping in Python to find additional vectors using a given initial condition

My question relates to looping in Python. I have an original $6$-sized vector, $F(n,t=0)=[1,0,0,0,0,0]$ Hence, the $n$-values range from $0 \rightarrow 5$. This output for the original vector is just ...
2
votes
2answers
147 views

Generating particles from a distribution function using Monte Carlo

I have been given a 4D ($x, y, v_x, v_y$) distribution function, $f(x,y,v_x, v_y)$, generated by an external code. I want to generate a set of particles from this distribution function, say 10k ...
2
votes
0answers
71 views

Divergence on wave equation simulation

I'm currenly working on my own PDE solver for non-linear simulations in python. I've done succesfully simulations for KdV and Fisher's equation, but now I'm playing with second order derivatives in ...
-1
votes
1answer
107 views

illegal use of ODEINT

given the following system: $$\frac{dP}{dt} = \alpha P(1-\frac{P}{K}) - \beta P I$$ $$\frac{dI}{dt} = \beta P I - \rho I$$ how do I solve the system numerically. as when I attempt to solve this is the ...
-1
votes
1answer
113 views

Implementation of Source Panel Method as Described in Katz Plotkin Book

I am currently trying to implement Source Panel method as described in Katz and Plotkin in Low Speed Aerodynamics. I have successfully implemented two previous methods. However, I am fully blocked on ...

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