# Questions tagged [scipy]

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

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### 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 ...
3answers
5k views

### How are scientific computing workflows faring on Apple's M1 hardware

The initial wave of reviews for Apple's M1 hardware are out, and there's lots of generic benchmarks and data on workflows on professional programs for creative users, but I haven't seen anyone talking ...
2answers
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### 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 ...
1answer
1k views

### Can an approximated Jacobian with finite differences cause instability in the Newton method?

I have implemented a backward-Euler solver in python 3 (using numpy). For my own convenience and as an exercise, I also wrote a small function that computes a finite difference approximation of the ...
5answers
10k views

### Dynamically ending ODE integration in SciPy

I have a light ray moving through space-time, i.e. a curve in $\mathbb{R}^4$, parametrized by some variable λ. The exact trajectory, i.e. the coordinate functions $x^μ(λ)$ of the curve are given by ...
1answer
627 views

### Matrix Balancing Algorithm

I have been writing a control system toolbox from scratch and purely in Python3 (shameless plug : harold ). From my past research, I have always complaints about ...
1answer
310 views

### Forcing an ODE solver to preserve the norm

I have an ODE of the form $$\frac{dy}{dt} = -i H y \enspace .$$ where $y$ is a complex vector and $H$ is a time dependent Hermitian matrix. The norm of the solution $y(t)$ at any point in time ...
3answers
4k views

### What does Python offer for distributed/parallel/GPU computing?

Using the SciPy/NumPy libraries, Python is a pretty cool and performing platform for scientific computing. I just wonder: When I have to go parallel (multi-thread, multi-core, multi-node, gpu), what ...
1answer
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 $(1,1000)$....
1answer
2k views

### Numerical solution of Geodesic differential equations with Python

I have made a solver based on the SymPy.diffgeom library, where I use Scipy.Integrate to solve the following system of second order differential equations : \begin{align} u'' &+ \Gamma^0_{00}(u')...
2answers
1k views

### Minimum path on known potential surface

I'm searching for the minimum path between the minima of a potential surface that is already known on a grid. (source: http://www.math.nus.edu.sg/~matrw/string/) Any point on the path is at an ...
4answers
20k 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 ...
4answers
6k views

### Algorithm for high quality 1/f noise?

How can I generate arbitrarily high quality $1/f$ noise, for use in a model? My model involves a lot of feedback, over a large number of iterations, with a very high bandwidth, so I'd like the $1/f$ ...
1answer
810 views

### Why does LSODA fail to integrate the logistic function?

I'm comparing some of the different ODE integrators in scipy.integrate.ode on solving the logistic function: $$x(t) = \frac{1}{1+e^{-rt}}$$ $$\dot{x} = rx(1-x)$$ ...
2answers
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2answers
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### SciPy interpolation with Univariate Splines

I have coded a routine for interpolation with B-splines, only to discover later that this functionality is already included in Python's SciPy. However, I do not understand one parameter in the SciPy ...
1answer
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1answer
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### Quantify integration error of scipy ode / ODEPACK

I am trying to integrate a 2nd order ODE with potential several singularities using the lsoda solver wrapped in scipy.integrate.ode(). I would like to put an error bar on the solution or at least ...
0answers
121 views

2answers
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### scipy odeint: sum of conservative ode equations does not remain zero as it is being solved — is this normal?

Let us say we have the following equations: dy1/dt = f(y1, t)  dy2/dt = g(y2, t)  The equations are such that they are "conservative", i.e. the ...
2answers
385 views

### Moore-Penrose pseudoinverse of singular rank degenerate matrix

I am trying to attain the Moore-Penrose pseudoinverse of a very large, very sparse, rank-degenerate, singular, and square matrix. ($75000 \times 75000$, near rank). The matrix is a graph Laplacian and ...
2answers
16k 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 ...
1answer
96 views

### Plotting optimum as a function of parameter in the objective

I am trying to minimize a 2d function using scipy.optimize. Specifically I want to plot the minimum value of the function fun as a function of the parameter wjk. The problem is that I cannot pass wjk ...
1answer
193 views

### Scipy Spline Interpolation Parameter

Documentation in scipy.interpolate (found at https://docs.scipy.org/doc/scipy/reference/tutorial/interpolate.html) states: "The parameter variable is given with the keyword argument, u, which ...
0answers
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5answers
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### Fast c++ library to solve very big sparse systems

I am working on a project with electrical circuits, where I am trying to compute the voltages at all the nodes of an electrical circuit. I know that the electrical circuit is a perfect grid, so each ...
2answers
2k views

### Scipy OdeInt solver with Neumann boundary conditions

I'm using scipy.odeint to solve Fisher-Kolmogorov equation: \begin{equation} u_t = u_{xx}+u(1-u) \end{equation} The code can be found here. From Ablowitz and ...
1answer
1k views

### Numerical derivative in python

I am trying to take the numerical derivative of a dataset. My first attempt was to use the gradient function from numpy but in that case the graph of the derivative ...
1answer
373 views

### Get the roots of a Hermite interpolating polynomial

I am using Python 3.7 to write a program that requires me to calculate the root of the Hermite interpolating polynomial, given two points $\epsilon_0$, $\epsilon_1$, the function ($d(\epsilon_0)$,\$d(\...