# Questions tagged [python]

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

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177 views

### Storing large amounts of interpolation data

Overview and Prior Research I am looking for a way store a (in principle arbitrarily) large "3D-table" for interpolation/ lookup in combination with python. I have considered CSV files, but,...
22 views

### Logistic growth curve using scipy is not quite right

I'm trying to fit a simple logistic growth model to dummy data using Python's Scipy package. The code is shown below, along with the output that I get. The correct ...
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### Why Is This Python Code Faster Than Fortran Wrapper with F2PY?

I am writing a proof-of-concept implementation of Newton's method for minimizing the negative log-likelihood term in a logistic regression model. I'm comparing the performance of a native python ...
37 views

### Numerically solving schrodinger equation [duplicate]

Consider the potential given above: $$U(r) = \frac{U_0}{\exp[(r - r_0)/\epsilon] + 1}\, .$$ How to solve the Schrodinger equation with this potential numerically and find the eigenvalues?
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### How to compute Singular value decomposition of a large matrix with Python

Language: Python3 Problem: I have a matrix Q of shape [51200 rows x 51200 cols] stored in a binary file, each of the element in this matrix has a data type of complex64. To load the data into memory I ...
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### Applying the result of Cuthill-McKee in SciPy

I have applied SciPy's implementation of the Cuthill-McKee algorithm to a $48 \times 48$ sparse non-symmetric matrix in Compressed Sparse Row (CSR) format and the output is an array of length $48$ ...
164 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 ...
220 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: ...
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### 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. ...
223 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 ...
736 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 ...
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### 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 ...
16k views

### Recommendation for Finite Difference Method in Scientific Python

For a project I am working on (in hyperbolic PDEs) I would like to get some rough handle on the behavior by looking at some numerics. I am, however, not a very good programmer. Can you recommend ...
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### 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 ...
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### 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-...
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 ...
115 views

### Reason behind different outputs for Fast Fourier Transform in Numpy and Matlab

Here is the output of Numpy np.fft.ifft([0, 4, 0, 0]) array([ 1.+0.j, 0.+1.j, -1.+0.j, 0.-1.j]) # may vary Here is the output of Matlab ...
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### Numerical solution to the infinite well problem

I've used the following code to implement it ...
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### 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 ...
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### 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 ...
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### Another way to evaluate the gravitational force from a uniform cube?

Appendix A of Liu, Baoyin, and Ma (2011) Equilibria, periodic orbits around equilibria, and heteroclinic connections in the gravity field of a rotating homogeneous cube shows an analytic expression ...
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### 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 ...
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### Determining the voxels between two boundary surfaces

Issue description I am working on human brain tACS simulations where I have the models of the skin, skull, csf, brain and ventricles in STL format. The shape does not matter and there are no ...
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### 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 ...
178 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 ...
177 views

### Pseudospectrum of non square Matrix in Python

I have a rectangular matrix $A \in \mathbb{R}^{m \times n}$ ...
57 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 ...
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### 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{...