# Questions tagged [python]

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

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8k views

### Understanding how Numpy does SVD

I have been using different methods to calculate both the rank of a matrix and the solution of a matrix system of equations. I came across the function linalg.svd. Comparing this to my own effort of ...
525 views

### Eigenvectors of a small norm adjustment

I have a dataset that is slowly changing, and I need to keep track of eigenvectors/eigenvalues of its covariance matrix. I've been using scipy.linalg.eigh, but it'...
47k views

### Python vs FORTRAN

Which one is better: FORTRAN or Python? And I guess that in both cases you need Gnuplot, am I right? I'm working on a Windows machine at the moment. I'd like to use it to get numerical solutions for ...
5k views

### When is Newton-Krylov not an appropriate solver?

Recently I have been comparing different non-linear solvers from scipy and was particularly impressed with the Newton-Krylov example in the Scipy Cookbook in which they solve a second order ...
6k 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! $k$...
296 views

### Heisenberg Model python : Specific heat capacity for spin 2

I have the correct plot for specific heat capacity when I am using the formula which is $C_V$ = differentiation of entropy with respect to temperature. However, When I try to calculate $C_V$, by using ...
619 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 ...
5k views

I am self teaching myself python and computational physics via Mark Newmans book Computational Physics the exercise is 2.9 of Computational Physics I have to compute the Madelung constant. . I have ...
25k views

### What is the preferred and efficient approach for interpolating multidimensional data?

What is the preferred and efficient approach for interpolating multidimensional data? Things I'm worried about: performance and memory for construction, single/batch evaluation handling dimensions ...
3k views

### Parallel Scientific Computation Software Development Language?

I want to develop a parallel scientific computation software from scratch. I want some thoughts on which language to start. The program involves reading/writing data to txt files and doing heavy ...
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 ...
2k views

### What is a good way to run parameter studies in C++

The problem I'm currently working on a Finite Element Navier Stokes simulation and I would like to investigate the effects of a variety of parameters. Some parameters are specified in an input file ...
2k views

### (how to) write simulations that run faster?

I have started using python as the programming language for doing all my assignments in CFD. I have a very little experience in programming. I am from mechanical engineering background and am pursuing ...
28k views

### Define custom probability density function in Python

Is there a way, using some established Python package (e.g. SciPy) to define my own probability density function (without any prior data, just $f(x) = a x + b$), so I can then make calculations with ...
6k views

### What language should I use when teaching an undergraduate course in computer programming?

Going to teach students of undergraduate level a course titled Introduction to Computer Programming. I am confused a bit. In Computational Physics scientists use C/C++ or Python or Fortran,CUDA etc.......
2k views

### Efficiency of using petsc4py vs. c/c++/fortran

How much slower is petsc4py vs c/c++/fortran? I realize it will depend significantly on the code being executed, but what about something simple like a matrix-vector product?
20k views

### Visually appealing ways to plot singular vector fields with matplotlib or other foss tools

What is the best way to get a visual appealing plot of a singular vector field (if you want to visualize also the field strength). As an example I am playing with the electric fields of two point ...
3k views

### How to compute the wavelet approximation of a function?

For the function $f(x)=x$, how to compute the wavelet approximation using Haar basis? I'm new to wavelet, I'm looking for a package which will do something like this ...
4k views

### Python OSS alternatives for Matlab Neural Network Toolbox. Any intercomparisons?

I'd like to be independent of commercial software for my scientific work. I find a dependence an commercial packages such as Matlab and its toolboxes unsatisfactory, because I do not know if I will ...
11k views

### What is the fastest way to compute all eigenvalues of a very big and sparse adjacency matrix in python?

I'm trying to figure out if there is a faster way to compute all the eigenvalues and eigenvectors of a very big and sparse adjacency matrix than using scipy.sparse.linalg.eigsh As far as I know, this ...
8k views

### Python implementations of Gillespie's direct method

I'm looking for a decent implementation of Gillespie's Direct Method in Python, as if I code the algorithm myself I'm nigh positive I'll do it inefficiently. Anyone have a favorite?
12k views

### Rearrange an ordinary matrix to block diagonal form

Is there an algorithm to rearrange a matrix into block diagonal form, given that the matrix is block diagonal in nature but randomized with an unwise choice of basis? In particular, are there any ...
4k views

### Poisson equation with Neumann boundary conditions

I'm trying to solve the Poisson equation with pure Neumann boundary conditions, $$\nabla^2\phi = \rho \quad in \quad \Omega\\ \mathbf{\nabla}\phi \cdot \mathbf{n} = 0 \quad on \quad \partial \Omega$$...
1k views

### Comparing Algorithmic complexity, ODE Solvers (Big O)

I am currently using the following three methods to solve differential equations: 4th order Runge Kutta Method Euler Method Internal scipy methods: ...
1k views

### Soft Question: Where does Python fit into the picture?

So I've been debating whether or not I should bother learning Python. From speaking with my professors, Matlab seems to be the common language used in applied mathematics/computational science as far ...
19k views

### scipy.optimize.fmin_bfgs: "Desired error not necessarily achieved due to precision loss"

I am getting the warning in the post subject when attempting to optimize a function in Python with the scipy.optimize.fmin_bfgs function. The complete output: Warning: Desired error not necessarily ...
21k views

### Plot integral function with scipy and matplotlib

I want to plot a numerical integral function of some function $f$ using scipy and matplotlib. How can I do this? I tried the ...
3k views

### Logistic regression with Python

I am trying to code up logistic regression in Python using the SciPy fmin_bfgs function, but am running into some issues. I wrote functions for the logistic (...
2k views

### How to plot orbit of binary star and calculate its orbital elements?

I have a set of dates, position angles ($\theta$) and angular separations ($\rho$) for visual binary star. For example: ...
142 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 ...
4k views

### Numerical evaluation of an elliptic integral in python

Goal: I need to evaluate numerically an integral of the following form: $$\int_0^\infty \frac{dx}{(a^2+x)\sqrt{(a^2+x)(b^2+x)(c^2+x)}}$$ where $a,b,c \in \mathbb{R}$ are in the interval $(1,1000)$....
3k views

### Efficiently finding all (x,y,z) points within certain distance of point P

I am using Python, and I have a Pandas dataframe with hundreds of thousands, if not millions, of $(x,y,z)$ coordinates. I am looking to find an efficient method to index the original dataframe so that ...
1k views

### Finding the first N roots of transcendental equation

I need to find the first $n$ roots of the transcendental equation \begin{equation} F(k) = J_m'(kr)Y_m'(k)-J'_m(k)Y'_m(kr) \end{equation} for integer values of $m$ and any $r \in [0,1)$ where $J'$ ...
944 views

### Compute lengths of the longest edge of each cell

Having mesh = UnitSquareMesh(2, 2) Q = FunctionSpace(mesh, 'DG', 0) this works as expected ...
166 views

222 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 ...
258 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 ...
4k views

### Python implementation for Frechet Distance

I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Frechet Distance algorithm for trajectory analysis, each trajectory has ...
11k views

### Using scipy.quad to calculate difficult integral

When evaluating the integral below in python using scipy.quad I get the following warning: UserWarning: The maximum number of subdivisions (50) has been achieved. If increasing the limit yields no ...
2k views

### How to express this complicated expression using numpy slices

I wish to implement the following expression in Python: $$x_i = \sum_{j=1}^{i-1}k_{i-j,j}a_{i-j}a_j,$$ where $x$ and $y$ are numpy arrays of size $n$, and $k$ is a numpy array of size $n\times n$. ...
5k views

### FEniCS: how to specify boundary conditions on a circle inside 2D mesh

I would like to numerically find a mutual capacitance of two stripes of metal on the opposites sides of a cylinder. The problem is obviously a 2D Laplace equation. I would like to find the potential ...
2k views

### Efficient eigen-decomposition of covariance matrix

I am looking for an C/C++/Python algorithm implementation that calculates eigenvalues and eigenvectors of a symmetric, positive semidefinite covariance matrix. A general-purpose eigen-decomposition ...
943 views

### Python package for (adaptive) function plotting

Are there any mature Python packages that can plot functions, and possibly use adaptive sampling? I am looking to pass only a function (can be a numerical black box) and a range, and expect a plot as ...
462 views

### Symmetric sparse direct solvers in scipy

scipy.linalg.solve, in its newer versions, has a parameter assume_a that can be used to specify that the matrix $A$ is symmetric ...
409 views

### Iteratively finding both left and right eigenvectors for non-symmetric complex matrix

I have a complex, non-Hermitian matrix $\mathbf{A}$, for which I need to find a few eigenvalues and eigenvectors in the generalised eigenvalue problem: \mathbf{A}\cdot \mathbf{x} = \lambda \mathbf{...