Questions tagged [scipy]
SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.
164
questions
0
votes
0answers
8 views
Scipy minimization failing with inequality constraints or bounds
I am trying to use scipy.optimize to solve a minimizaiton problem but getting failures on using an inequality constraint or a bound. Looking for any suggestions regarding proper usage of constraints ...
0
votes
1answer
48 views
How to use cumtrapz correctly?
I have tried to do a trapeze integration with f(x)=x^2, where I know how the antiderivative looks like, so F(x) = (1/3)x^3
Here's my code, just like I tried:
...
0
votes
0answers
48 views
Applying the result of Cuthill-McKee in SciPy (followup)
This is a followup to Applying the result of Cuthill-McKee in SciPy , where I'm not sure the answer given is correct. It's also 4 years old, so I'm trying a new question. The question is still ...
2
votes
0answers
30 views
Non-negative Least Squares to perform Inverse Laplace with weights
I'm trying to perform the inverse Laplace transform of a (noisy) dataset $y_i$ using Tikhonov regularization:
$$\min \sum_{i=1}^{N} \left(\int_0^\infty e^{-s_i t} f(t) \, dt - y_i \right)^2 - \lambda^...
0
votes
0answers
36 views
scipy's solve_ivp returns erroneous results for a stiff differential equation
I'm using scipy's solve_ivp for solving a stiff differential equation. I'm using method BDF for solving the same.
I have already used MATLAB's ode23s and I'm getting correct results in MATLAB.
However,...
0
votes
0answers
73 views
A parallelized GMRES solver?
My application calls for solving a dense, 40,000 x 40,000, ill-conditioned linear system. The native SciPy GMRES solver with preconditioning has worked well for my application and solving a single ...
1
vote
1answer
141 views
Is LAPACK behind the cutting edge of dense linear algebra?
I have been digging into some numerical linear algebra lately, and reading in particular about how LAPACK solves symmetric eigenvalue problems. I noticed that the ...
0
votes
0answers
25 views
Comparing custom linear regression solver to SciPy equivalent in Python
From a given data set, I set out to complete a task which is below
Fit the data of the previous exercise to fit Eq. (8.18) using the SciPy function ...
2
votes
1answer
62 views
Functions from Scipy, Blas, or Lapack that compute only upper triangular matrix
My goal is to transform a matrix into upper triangular form in Python. I know the function scipy.linalg.lu will do LU decomposition and get both upper and lower ...
3
votes
1answer
129 views
Why is 'scipy.sparse.linalg.spilu' less efficient than 'scipy.linalg.lu' for sparse matrix?
I have a matrix B which is sparse and try to utilize a function scipy.sparse.linalg.spilu specialized for sparse matrix to ...
5
votes
1answer
141 views
Algorithm to factorize matrix whose many rows are already of upper triangular form?
I have a matrix whose many rows are already in the upper triangular form.
$$\begin{bmatrix}
x_{11} & x_{12} & x_{13} & x_{14} & x_{5} \\
0 & x_{22} & x_{23} & x_{...
3
votes
1answer
96 views
Computing numeric derivative via FFT - SciPy
I wrote the following code to compute the approximate derivative of a function using FFT:
...
3
votes
1answer
51 views
Fast nonzero indices per row/column for (sparse) 2D numpy array
I am looking for the fastest way to obtain a list of the nonzero indices of a 2D array per row and per column. The following is a working piece of code:
...
0
votes
0answers
10 views
How to optimize linear programming subproblems with respect to global constraints?
I have an optimization problem where I have several categories and for each category $j$ I have entries $i = 1....m$, I wish to assign some value $x_{ij}$ for each entry of each category but:
I need ...
0
votes
0answers
19 views
How to plot a function for multiple values of a parameter in the same set of axes in Python?
I'm currently trying to plot a graph wich describes a photoionization cross section as a function of incident photon energy for optical transition in a semiconductor for different values of the $\...
1
vote
1answer
36 views
How do I get scipy.minimize to terminate below a certain loss threshold?
I was looking at the scipy.minimize documentation to see if I could find a way to terminate optimization when the loss gets below some cut-off, and I couldn't see ...
5
votes
0answers
97 views
How to numerically evaluate this double Integral?
I want to evaluate the following integral:
$$\int_{0}^{60} \ \left(\int_{0}^{2z} 0.5\cdot t \left(\mathrm{erf}(t-a) -1 \right)J_{0}(qt)\mathrm{d}t \right)^2 \mathrm{exp}\left(-\frac{(z-a)^2}{2s^2}\...
0
votes
1answer
45 views
Solving an ODE using odeint in Python and continuing the integration
The following relates to the linked question:
Scattering of waves in a symmetrical potential (using python)
I have attempted to solve the problem for $U(r)$ using ...
0
votes
1answer
26 views
How to change the value of a variable at some point lying in the time interval of solver in solve_ivp
The following code solves a differential equation with scipy:
...
0
votes
1answer
47 views
solve_ivp - Overflow encountered in double_scalars
I'm modeling an electron that orbits the nucleus. Of course, charged particles radiate away there energy so it'll crash into the nucleus. My approach has been to to evaluate the coulomb force and add ...
2
votes
1answer
33 views
How to implement Simpson's rule for double integral (without numeric limits of first integral)
I want to use Simpson's rule to evaluate the following double integral:
$$\int_{a}^{b}\left|\int_{0}^{z}x\cdot \mathrm{erf}(x-10)\cdot J_{0}(x) \mathrm{dx}\right|^{2}\exp(-0.5*(z-40)^2)\mathrm{dz} $$
...
0
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0answers
32 views
Scipy.integrate.odeint is returning curves with almost the same frequency for different damping ratios, shouldn't they be different?
I am trying to solve the ODE for a harmonic oscillator using Scipy's odeint solver for different dampening factors.
I'm using the following code, based off of this example:
...
2
votes
1answer
34 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 ...
1
vote
1answer
88 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 ...
0
votes
0answers
21 views
Can Scipy.optimize take a user-defined objective function that contains an ML model?
I have an optimization task that requires me to choose the optimal combinations of parameters, according to the prediction of a random forest model. My main obstacle is that scipy.optimize always ...
-1
votes
1answer
53 views
Plot of a function involving an integral and value changing parameters [closed]
I'm trying to plot the cross section with respect to the photon energy $h\nu$ but for $\gamma = 1.0, 1.2, 2.0 $ in the same axes
$\sigma = \left[\left(\frac{\xi_{eff}}{\xi_{0}}\right)^2 \frac{n_r}{\...
5
votes
1answer
173 views
How to know which LAPACK's function is used by Scipy's eig function?
As far as I understood, scipy.linalg.eig use wrappers from scipy.lapack to compute the eigenvalues and eigenvectors of a matrix. ...
5
votes
1answer
80 views
How do I globally change the precision of a piece of code in Python to debug it?
I am solving a system of non-linear equations using the Newton-Raphson method in Python. This involves using the solve(Ax,b) function (...
0
votes
1answer
106 views
Solving differential equation in Python with discretized variable coefficients
I am trying to solve a differential equation with discretized variable coefficients which are calculated from a time serie.
In this case the Runge-Kutta step size is fixed by the frequency in the time ...
2
votes
1answer
66 views
How to set up a time-dependant matrix for an ODE to be solved using python?
I want to solve a problem numerically in python like this:
$$
y(t)' = \mathbf{M}(t)y ,\\
y(0) = (1,0,0,0 ...)
$$
where $y$ is an $n$-dimensional vector and $\mathbf{M}(t)$ is a time-dependant $n \...
5
votes
0answers
168 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 ...
0
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0answers
18 views
How to handle system of chemical reactions for a batch reactor SciPy solver
I have a system of chemical reactions where the rate equations represent a batch reactor model. The model is a system of ODEs which is solved with the SciPy ...
3
votes
1answer
235 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 ...
1
vote
1answer
167 views
Runge-Kutta fourth order method. Integrating backwards
I am using a Runge-Kutta fourth order method to solve numerically the usual equation of motion of a background scalar field in curved spacetime with a quartic potential:
$\phi^{''}=-3\left(1+\frac{H^{...
3
votes
1answer
114 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 ...
3
votes
1answer
83 views
Conjugate Gradient for singular 2D poisson finite element with Neumann Boundary Conditions
Heavily edited question after I realised partly what the problem was
I have programmed a simple 2D square finite element solution to the Poisson equation
$-\Delta u = f$
The source function ...
5
votes
3answers
148 views
Maximize a function of an orthogonal matrix
I'm trying to write up a small code that, given a set of normal vibrational modes for a molecule, will convert them to localized vibrational modes. To do this I'm following the procedure from J. Chem. ...
6
votes
2answers
1k views
Is there an efficient way to form this block matrix with numpy or scipy?
Is there an efficient way to form this block matrix with numpy or scipy?
$$
\left[
\begin{array}{cccc}
\mathbf{B} & \mathbf{0} & \cdots & \mathbf{0}\\
\mathbf{AB} & \mathbf{B} & \...
1
vote
1answer
147 views
Preconditionning for solving a non-linear system of equations with least squares
I am trying to solve a large system of non-linear equations (about a few hundred equations and variable but with less variable than equations). Given that the system is really sparse and large I am ...
3
votes
1answer
225 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(\...
4
votes
2answers
1k views
Numerical evaluation of a Gaussian Integral in Python?
Goal
I'm trying to write code to compute the normalized Gaussian in the following,
$$
\begin{equation}
\int_{-\infty}^{\infty} \frac{1}{ \sigma \sqrt{2 \pi}} \exp\bigg( - \frac{(x - \mu)^{2}}{2 \...
1
vote
2answers
71 views
identifying peaks in data
I have data with peaks on some background, for example:
The two prominent peaks at ~390 and ~450, as well as the much smaller peak at ~840. What are some options to programmatically find the position ...
3
votes
1answer
357 views
Plug-and-go Clebsch-Gordan computation in python?
I started a little project in python, under the assumption that it would be easy to find a routine for numerically computing Clebsch-Gordan coefficients in some library such as scipy. When it came ...
2
votes
1answer
338 views
Forward and backward integration — cause of errors
I write a test program to integrate foward on $[0,T_f]$ and then backward on $[T_f,0]$ from the endpoint of the forward integration an Hamiltonian system:
$$
\dot q(t) = \frac{\partial H}{\partial p}(...
1
vote
0answers
48 views
Finite dimensional optimization problem over dynamical system
I am interested in solving numerically the following mathematical problem
Consider an ode of the form
$$
\dot q(t) = f(q(t),t_1,\ldots, t_N),\qquad t\in [0,T],
$$
where $q\in \mathbb{R}^n$ is the ...
2
votes
1answer
153 views
User friendly scipy optimize wrapper package?
I'm creating too much throw away code for interfacing with the scipy optimize package in a user friendly way. (See code below for example of interruptible optimization that keeps last optimization ...
3
votes
1answer
153 views
Poisson image blending artifacts
I am trying to implement Poisson image blending as in the paper Poisson Image Editing. This is the task of filling in a masked region of an image by minimizing
$$\min_f\int_\Omega \left | \nabla f - \...
2
votes
0answers
38 views
ILUTP in sparse.linalg.spilu?
In Matlab, an ILU with threshold and pivoting (ILUTP) can be passed by default as:
setup.type = 'ilutp';
[L, U] = ilu(A, setup);
Looking for an equivalent in ...
0
votes
0answers
41 views
Time sampling changes solution
I'm currently trying to solve a problem using numerical methods. The set-up is rather long, so I apologize in advance...
TL;DR: My solutions change depending on how big my steps are and I don't know ...
3
votes
4answers
474 views
Numerical integration in Python with unknown constant
I’d like to solve the below equation for the unknown $T$:
$$\int_0^\infty \frac{x^2}{\exp\left(\frac{x}{T}\right)-1}\kappa_x \mathrm{d}x = C,$$
where $C$ is a known constant and $\kappa_x$ is some ...
