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Questions tagged [scipy]

SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.

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37 views

Find peaks method for finding elusive peaks

I'm currently utilizing the find_peaks function to identify peaks within this spectrum. However, despite consulting similar queries on Stack Overflow, my attempts to incorporate features such as ...
0 votes
0 answers
42 views

How to calculate the numerical integration and plot the result in python?

I am trying to solve the question below in McQuarrie Physical-Chemistry book. The first step of the exercise, I solved. However, the second step involves a numerical integration. I can develop a code ...
0 votes
1 answer
66 views

BSplines from scipy not defined on whole range of the knots

I am looking at the construction of BSplines out of curiosity. I created a small code that uses scipy.interpolate.BSpline to create basic splines. I get the following basic splines for order 0, 1 and ...
2 votes
2 answers
6k views

WRL and VRML to Matplotlib/Numpy

I would like to import (or parse ??) a WRL/VRML file format in python in order to work the data with Matplotlib. Is there any way of converting this file format into plottable numpy arrays ? I ...
0 votes
1 answer
48 views

solve_ivp method=ODE23 time step not decreasing in order

My time step with the function scipy.integrate.solve_ivp is not decreasing in t_span fluctuating (reaching values below or ...
2 votes
1 answer
120 views

Different Results for Double Pendulum

In this study, (Hidden Fractals in the Dynamics of the Compound Double Pendulum) the authors provide various fliptime fractals (of a double pendulum) for different length combinations. However, when I ...
0 votes
2 answers
59 views

scipy exp model fitting: prevent coefficients blowup

I'm trying to fit a few X-Y points that look like exponential. I used the following scipy code: ...
2 votes
0 answers
65 views

Hyperbolic integral of the second kind

The elliptic integral of the second kind is given by $$ E(t,m) = \int_{0}^t \sqrt{1-m \sin(s)^2} \operatorname{ds} $$ and there is for instance a scipy function ellipeinc that computes it. The ...
0 votes
2 answers
121 views

BFGS Constrained Optimization Failure Due to Precision Loss

I am trying to optimize the following objective function according to some constraints. However, the optimization fails at the first iteration with the message that the desired error was not ...
0 votes
0 answers
35 views

using scipy.sparse.linalg.eigsh for degenerate states in Bose Hubbard model

I am currently writing a code for the Bose-Hubbard model, and I am calculating the ground states and single-particle density matrix for different values of U and J. As U=0, one would see how the ...
1 vote
2 answers
436 views

optimizing piecewise linear objective functions (perhaps non convex) with equality constraints

When I do my project, I need to optimize piecewise linear objective functions (perhaps non convex) with equality constraints. The piecewise linear objective function may be not convex like this in the ...
0 votes
0 answers
97 views

How to minimize a numerical integration in python?

I need some help to minimize a numerical integration. It's about a classical problem in physics (hydrogen atom). It can be solved analytically but I need to solve it numerically in Python. We have an ...
0 votes
0 answers
69 views

Singular Matrix Error in Incomplete LU Decomposition

I’m currently working on solving the following PDE: $$\begin{equation} -(\mu_x \frac{\partial^2 u}{\partial x^2} + \mu_y \frac{\partial^2 u}{\partial y^2}) = f(x, y)\end{equation}$$ Where a right hand ...
5 votes
2 answers
2k views

What algorithm(s) do numpy and scipy use to calculate matrix inverses?

I am solving differential equations that require inverting dense square matrices, and I wanted to know what algorithm(s) do numpy and scipy use to calculate matrix inverses?
0 votes
1 answer
79 views

How to use a custom OdeSolver in Scipy's solve_ivp

In Scipy's solve_ivp documentation, we see the method argument can be either a string or a user-defined ...
2 votes
1 answer
93 views

Numerical calculation of Lyapunov exponents using SciPy's built-in solve_ivp

I have previously successfully implemented the QR decomposition method in MATLAB to calculate Lyapunov exponents for Lorenz equations. See here. This method integrates the stacked system, i.e. the ...
4 votes
3 answers
28k views

scipy odeint - Excess work done on this call

I'm newbie both in calculus and Python/Scipy so I apologize if this question is too dumb. I'm trying to model flow between two pressure vessels. Let's say we have two points and a link between them ...
5 votes
2 answers
464 views

Number of function calls and jacobian calls in scipy.root

Just as an exercise, I am numerically solving the following system of equations: $$ \begin{equation} \begin{cases} x^2 + y^2 = 32 \\ 3x + 7y = 15 \end{cases} \end{equation} $$ ...
6 votes
3 answers
4k views

Computing numeric derivative via FFT - SciPy

I wrote the following code to compute the approximate derivative of a function using FFT: ...
16 votes
3 answers
17k 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 ...
0 votes
0 answers
139 views

Solving system of ODEs, where time derivative approaches infinity due top initial condition

I am trying to solve a problem in python using scipy's solve_ivp. The system of ODEs I am trying to solve is for coupled where I am solving for two time-dependent ...
2 votes
1 answer
140 views

Weights for equidistant samples in power law fitting

I am working on fitting analytical curves to experimental data obtained in real viscoelastic tests (in fact, static creep tests). The setting of the problem is: the experimental data I have is a set ...
2 votes
1 answer
207 views

2D integrals in Python with specified points of interest

Note: This is my first question on stackexchange; please tell me if I'm doing something incorrectly. I am trying to calculate a series of a 2D integrals in Python with an integrand that has several ...
2 votes
2 answers
1k views

Why does `scipy.optimize.minimize(...)` fail with this toy constrained minimisation case?

I'm learning scipy.optimize.minimize. I thought of a simple function to see how it works: $$f(x) = x$$ With the goal to minimise $f(x)$, subject to the constraint ...
1 vote
0 answers
250 views

Using solve_ivp for a PDE: how to handle multiple time-dependent variables?

I am trying to build a Python code that solves a set of coupled differential equations which will be spatially discretized by the method of lines advancing in time. I am planning to use ...
2 votes
2 answers
411 views

Solving IVP backward in time via python

I'm having difficulty solving an initial value problem (IVP) in Python backwards in time. The code is at the end of this post. First, please let me state my simplified problem. The forward IVP is ...
0 votes
0 answers
27 views

Matching the limits of integration with the proper variables in a complicated case when using scipy.integrate.nquad

I need to integrate expressions containing powers of the function: ...
2 votes
1 answer
4k views

Three dimensional irregular grid data interpolation to regular grid

I have three-dimensional radar reflectivity data obtained as voxels (scans, rays, altitudes). The data has been sampled at irregular spacings and I want to convert this into a regular grid. In ...
6 votes
1 answer
326 views

Accelerating the computation of scipy.sparse.linalg.expm_multiply

I have a tridiagonal antiHermitian matrix ($-i*Hami*t$) with nonzero elements only along the upper diagonal and lower diagonal, and the goal is to know the action of exponential of such matrix on a ...
2 votes
1 answer
636 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 ...
2 votes
2 answers
96 views

How do I evaluate the numerical solution at a point that isn't on the mesh

I'm trying to code a fixed-point method to solve the following system using scipy.integrate $$ u_{n+1}(s)=\int_0^TK_\lambda(t,s)\left(\lambda u_n(t)+\sigma(t)+f(t, ...
1 vote
1 answer
133 views

Possible bug with scipy.optimize SHGO sobol: TypeError: <lambda>() takes 1 positional argument but 3 were given

I have been trying to perform some global optimization with SciPy optimizer SHGO and I've had issues with the sampling method 'sobol'. Specifically, I get an error ...
0 votes
2 answers
60 views

How to program the convergence of a sequence of systems of integral equations using Scipy

I'm trying to solve the problem where $u_n$ and $v_n$ are sequences that converge to the solution $u$ and $v$ and $\lambda$, $\sigma$, $f$ and $g$ and K_lambda are all given. I thought of using the ...
2 votes
1 answer
215 views

Global convergence behavior of several Krylov solvers in scipy.opt

In the context of mechanical simulation, where I solve the stationary action principle directly (i.e. $\nabla S = 0$ for some scalar function $S$), I use the wrapper ...
1 vote
1 answer
363 views

How to perform FFT from plane-wave basis function coefficients to real space?

I have a 3D grid in real space of grid spacing $L$ and say 21 grid points in each direction, containing e.g. a charge distribution. This is stored as a numpy array of shape ...
-1 votes
1 answer
146 views

Solving Transcendental equation involving special functions becoming nightmare any one can help?

Simply i want to solve for schrodinger equation for finite potential well problems in spherical coordinates. For case in which l=0 . It is simple but when l changes. The solution are spherical ...
2 votes
1 answer
122 views

Need help to fully understand SciPy's odeint's reported step sizes, eval times, # of funct calls & total proc. time (re. question in Astronomy SE)

A recent question in Astronomy SE Numerical Programming using odeint takes more than 17 minutes got me interested in looking closer at SciPy's odeint. The problem is a modified orbital mechanical ...
0 votes
2 answers
492 views

Why is this scipy.root code not converging?

I'm running a test problem to set up larger problems. Solving the simple unsteady heat equation via finite differences: $$ \frac{\partial T}{\partial t} = \alpha \frac{\partial^2T}{\partial x^2}$$ $\...
2 votes
0 answers
139 views

Scipy.root not converging even when provided with initial guesses very close to solution

I've made a previous question here and also in SO wondering why only the fsolve solver converges for the simple one dimensional unsteady conduction problem $$ \frac{\partial T}{\partial t} = \alpha \...
0 votes
1 answer
168 views

Solve 1st order ODE in using `scipy`

I've been trying to solve the following equation $$ y(t)=-A\cdot\frac{\mathrm{d} y}{\mathrm{d} t}+B\cdot\left(\frac{\mathrm{d} y}{\mathrm{d} t}\right)^{2}+C \\ y(t=0)=y_{0}\\ $$ where $A$, $B$, and $C$...
1 vote
1 answer
93 views

Solving basic barystochrone problem in python

I am trying to solve $\frac{u''}{1+u'^2} - \frac{1}{2(1-u)} = 0$ subject to $u(0)=1, u(1)=0$. If I understand how to do this properly, I first do the variable substitutions: $u = y$, $y_1 = y; y_2 = y'...
3 votes
1 answer
123 views

Interpolating 2D data on a hemisphere in order to have $C^2$ function but no overshoot

I am interpolating a 2D dataset on a hemisphere, and I am currently using scipy.Rbf that I like for its simplicity. I am defining the norm of the interpolator with ...
1 vote
1 answer
709 views

Beta function and integral value

I have two values $a$ and $b$ where $a \ge 0$ and $b \ge 0$ and I have to calculate the formula below. $$ \frac{1}{2}\int_0^1\text{abs}\left[\left( \frac{p_i^{(a - 1)} \times (1 - p_i)^{(b - 1)}}{\...
3 votes
2 answers
2k views

Inaccurate results of integration using scipy solve_ivp

I am trying to use solve_ivp to solve the following 1st order ODE: $$ \frac{d \rho}{d z} = \frac{m \theta}{(1+\theta z)} \, \rho, $$ subject to $\rho(z=0)=1$, where ...
1 vote
2 answers
2k views

Fix step size with scipy.integrate.RK45 and scipy.integrate.LSODA

I am trying to numerically integrate a differential equation using scipy.integrate.RK45 and/or scipy.integrate.LSODA. Now, I am trying to fix the integration step sizes of both solvers. This, however, ...
3 votes
1 answer
1k views

Using the Kramers-Kronig (Hilbert) transform in Python

I am trying to use the Kramers-Kronig algorithm to transform the real and imaginary contributions to the anomalous scattering factor from a diffraction anomalous fine structure (DAFS) experiment. I ...
3 votes
1 answer
123 views

Scipy solve_ivp sensitivity to random phase shifts

I am trying to solve a coupled system of ODE's using the solve_ivp function from scipy. The general form of the equation is given via $$\dot{y}(t) = M(t)y(t).$$ The time dependence of matrix is ...
2 votes
1 answer
718 views

How to extract intermediate calculation results from an SciPy ODE function in python?

I have a bit lengthier ODE function which was simulated by using Scipy solve_ivp function. During this simulation I calculated many parameters but as the output, I am taking out put only some other ...
1 vote
1 answer
402 views

L2 norm optimization problem

I have an optimization problem where i need to find an image x, that is very close to x' such that: monitor(x') is valid but monitor(x) is invalid. (output is valid when the neural network output is ...
2 votes
0 answers
101 views

How to save multiplication computation time between a dense vector and a not that sparse matrix?

I am trying to compute $\mathbf{X}\mathbf{u}$ for many times in my algorithm, where $\mathbf{X}\in \mathbb{R}^{n\times m}$ and $\mathbf{u} \in \mathbb{R}^{m}$. The problem is that, during the ...

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