Questions tagged [scipy]

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

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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 ...
HWIK's user avatar
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2 votes
1 answer
79 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 ...
ren1's user avatar
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2 votes
1 answer
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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 ...
Feathers's user avatar
1 vote
0 answers
67 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 ...
Ziad Nasef's user avatar
2 votes
2 answers
170 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 ...
JesseJC's user avatar
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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: ...
ale victor's user avatar
6 votes
1 answer
148 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 ...
code437's user avatar
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1 vote
1 answer
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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 ...
Sasche's user avatar
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2 votes
2 answers
88 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, ...
tareqath's user avatar
0 votes
2 answers
42 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 ...
tareqath's user avatar
-1 votes
1 answer
110 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 ...
LEO PHYSICS's user avatar
2 votes
1 answer
100 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 ...
uhoh's user avatar
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2 votes
0 answers
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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 \...
Klaus3's user avatar
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2 answers
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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: $$ \frac{\partial T}{\partial t} = \alpha \frac{\partial^2T}{\partial x^2}$$ $\...
Klaus3's user avatar
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1 answer
134 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 $C$...
BackSpace42's user avatar
2 votes
2 answers
509 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 ...
caveman's user avatar
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1 vote
1 answer
88 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'...
Makogan's user avatar
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0 answers
582 views

ValueError: array must not contain infs or NaNs; When using solve_ivp in the scipy library

I am solving an initial value problem using solve_ivp. The problem consists of computing the concentration profile of a set of reactions over time, given the initial concentrations and some of the ...
HWIK's user avatar
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3 votes
1 answer
116 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 ...
Balfar's user avatar
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1 vote
1 answer
404 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)}}{\...
Bhavana Reddy's user avatar
1 vote
2 answers
875 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, ...
Octavius's user avatar
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3 votes
1 answer
93 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 ...
raeel's user avatar
  • 31
3 votes
1 answer
537 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 ...
ayrton burgess's user avatar
2 votes
1 answer
337 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 ...
Nis's user avatar
  • 21
2 votes
0 answers
94 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 ...
Xun Maoapo's user avatar
2 votes
1 answer
1k views

scipy.optimize.root not converging and RuntimeWarning

I am trying to solve the following problem: $$ \frac{d^2y}{dx^2}=\sinh(y) $$ Where the boundary conditions are: $y(0)=-1$, and $ \frac{dy(x\rightarrow \infty)}{dx}=0 $. Through central difference ...
HWIK's user avatar
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1 vote
1 answer
241 views

Finding the parameters of a function via curve fit

I'm trying to estimate the parameters (v, n, k) defined in fit_func. I tried the default least squares fit but I couldn't find the parameters successfully. ...
Natasha's user avatar
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0 answers
370 views

Curve fitting using a piecewise polynomial

I am trying to fit a piecewise polynomial function Code: ...
Natasha's user avatar
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0 votes
1 answer
49 views

Scipy QZ documentation

The scipy.linalg.qz function implements generalized Schur decomposition for a pair of matrices A, B such that (A, B) = (Q @ AA @ Z*, Q @ BB @ Z*), where ...
Amit Varshney's user avatar
0 votes
1 answer
771 views

Fitting a monotonically increasing spline function

I want to fit a monotonically increasing smooth spline function for a dataset Code: ...
Natasha's user avatar
  • 491
3 votes
2 answers
997 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 ...
Fryderyk's user avatar
1 vote
0 answers
169 views

SLSQP solver scipy with linear subset constraints

I have been trying to solve a least squares problem of the following form: $$ \begin{equation} \min_{\vec{x}} \frac{1}{2} \lVert f(\vec{x}) - f_{\text{target}} \rVert_{2}^2 + \alpha\Big( \frac{1-\rho}{...
bfg's user avatar
  • 11
1 vote
0 answers
85 views

Using absolute error as the cost function

This is related to my previous post Minimize distance between curves. I have a dataset with values of multiple curves. An example plot is shown below. I want to scale the curves (move up/down) so that ...
Natasha's user avatar
  • 491
0 votes
0 answers
152 views

Solving differential equations with fast oscillations using odeint

I have wrote this code to solve an equation , I know the behavior of this function has very rapid oscillations, when I RUN it gives bogus values for some "m[x]" and some "t"'s, ...
danial's user avatar
  • 11
1 vote
1 answer
261 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 ...
Protocola's user avatar
-1 votes
1 answer
123 views

Fitting gauss-hermite-parametrization to data?

I want to fit this data. I have the following model functions. Classic gaussian: def gauss_model(x, mu, sigma): return np.exp(-0.5*((x-mu)/sigma)**2) And ...
trynerror's user avatar
1 vote
1 answer
357 views

Huygens Fresnel Diffraction integral using dblquad in python

I am attempting to create a python function to assist in calculating the following numerical integration of the Huygens Fresnel integral in the form of ...
OmegaCentauri's user avatar
1 vote
0 answers
2k views

scipy.optimize.minimize fails to converge but result is OK

I am trying to optimize a non-linear least squares problem with scipy.optimize.minimize. I have simplified my actual problem down to the case where I am just computing the top 'principal components' ...
user32157's user avatar
  • 119
1 vote
1 answer
99 views

Parameter estimation simple theory question related to scipy.optimize.curve_fit

It has been a while since I have done some stats, and I have tried to fit a curve using optimize.curve_fit of parameter estimation. I am also interested in the standard deviation of the fitted ...
Daniel's user avatar
  • 99
1 vote
1 answer
1k views

Easy way to perform solver over pandas dataframe

I'm moving from Excel to Python and I'm trying to solve these equations: $$\begin{align} X_1&=\bigg[\big(3.47-\log(X_2)\big)^2+\big(\log(c)+1.22)^2\bigg]^{0.5}\\ X_2&=\frac{a}{101.32}\bigg(\...
JCV's user avatar
  • 113
2 votes
1 answer
313 views

2nd order differential equation coupled to integro-differential equation in python

I'm trying to solve the following equations numerically in python $$\begin{align} 12\pi\int_0^\infty drf(r)\phi(r)r^4&=E\\ f(r)-\frac{1}{2\mu}\bigg(\frac{d^2\phi(r)}{dr^2}+\frac{2}{r}\frac{d\phi(r)...
mmikkelsen's user avatar
0 votes
1 answer
2k views

Optimal value of parameter/s from a set by scipy.optimize.minimize() method

I have this function $y = \exp(-x)$. I have a list of $x$ values and corresponding $y$ values. ...
Pro's user avatar
  • 113
2 votes
1 answer
103 views

Finding the correct order of eigenvectors of a parameter-dependent Hermitian matrix

so, I have a symmetric, analytic matrix $\mathbf{H}(x)$ ($x$ is real). Because $\mathbf{H}(x)$ is analytic and $x$ is real, it is possible to find analytic functions for the eigenvectors and the ...
cheetah's user avatar
  • 153
2 votes
1 answer
115 views

SciPy ODR "Ordinary" Least Squares?

Scipy.odr has a setting for "fit types", including one for ordinary least-squares. This matches with the documentation of ODRPACK (see p. 31, Computational method). However, the package ...
Bernd's user avatar
  • 21
2 votes
1 answer
312 views

Can't solve second order differential equation with scipy

Most of my knowledge about numerically solving differential equations is long forgotten. Unfortunately I stumbled upon a physics problem where I need to do exactly that. I'm trying to describe the ...
Mr P's user avatar
  • 31
2 votes
1 answer
199 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 ...
G. Fougeron's user avatar
3 votes
1 answer
602 views

How to solve a BVP with known parameters?

I need to solve a boundary value problem (BVP) of second order, where the equation depends on several know parameters, which are geometric parameters and material constants. I would like to solve this ...
Ken Grimes's user avatar
1 vote
0 answers
247 views

Trouble inverting complex matrix with numpy and scipy

I have some matrix-valued, complex data $Z(f)$ with $f\in\{f_0,f_1,\dots\}$ and $Z(f_i)$ being a 3x3 matrix. I require the inverse $Z^{-1}(f)$ in my workflow. After encountering some problems with my ...
totally_lost's user avatar
5 votes
0 answers
106 views

How to troubleshoot numerical instability using finite difference for steady-state non-linear heat conduction equation

I have a problem which I believe is numerical instability when trying to solve a heat conduction equation using finite difference. The short version is that when the parameter $I=80.3$ I get the blue ...
Ken Grimes's user avatar
1 vote
1 answer
167 views

solve_ivp doesn't work with toms748

I have the following code ...
user7896's user avatar
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