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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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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
5 votes
0 answers
111 views

Check if LinearOperator is symmetric

I have a scipy.sparse.linalg.LinearOperator object. I'd like to check if its associated matrix is symmetric without actually instantiating the matrix in the most ...
Alex L's user avatar
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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 ...
Federico Poloni's user avatar
5 votes
0 answers
540 views

Optimisation of matrix exponential

I have a 7000x7000 sparse matrix (scipy), which I want to exponentiate. I've tried using scipy.sparse.linalg.expm, which works quite well for smaller matrices (takes a few seconds for a 1000x1000 ...
ferros's user avatar
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555 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{...
DaveP's user avatar
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0 answers
304 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}\...
Shankar_Dutt's user avatar
4 votes
0 answers
91 views

Large residual when integrating 2nd order ode close to singularity with SciPy ode / ODEPACK

I am trying to integrate a 2nd order ODE with a singularity at close to the initial condition. Why do I get large residuals when I plug-in the result of my integration back into the ODE? The equation ...
jensv's user avatar
  • 133
3 votes
0 answers
51 views

Pass forward intermediate results during iterative optimization

To investigate a counter-current flow heat exchanger while considering temperature dependent physical properties (such as specific heat $c_\textrm{p,i}$, heat conductivity $\lambda_\textrm{i}$, ...
albert's user avatar
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3 votes
0 answers
155 views

Does shift-invert method has invertibility issue?

Please note that I have nearly zero background on numerical methods. I understand the shift invert method as described in SciPy Tutorial The main argument of the above link is as follows. Suppose we ...
Laplacian's user avatar
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3 votes
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144 views

Difference between wave vector and density matrix in numerical calculation of Schrödinger equation

I solved Schrödinger equation for a following tow-level time-dependent Hamiltonian numerically in two ways: ...
wayna's user avatar
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3 votes
0 answers
158 views

Python routine to calculate shape resonances of H2

I am currently doing a project in which my aim is to write a program that can be used to calculate single and multi-channel shape resonances. So I'm looking at bound states and quasi-bound states. ...
Alon Shoshan's user avatar
3 votes
0 answers
462 views

Computing Small Eigenvalues with Sparse Symmetric Indefinite Mass Matrix

I want the eigenvalues of the following generalized eigenvalue problem: $$ Av = \lambda M v $$ where $A\in\mathbb{R}^{n\times n}$ is sparse, symmetric, and positive semi-definite $M\in\mathbb{R}^{n\...
user3658307's user avatar
3 votes
0 answers
104 views

Inconsistency in optimize.minimize

I am trying to fit a time-dependent curve at each time step. I do so in minimizing along $x_c$ the quadratic error between the curve and a reference solution $ 1/(1 + \exp\left(\sqrt{S}(x-x_c)\right) $...
bela83's user avatar
  • 443
3 votes
0 answers
389 views

Left eigenvectors using ARPACK

I'm trying to find both the dominant $k$ left and right eigenvectors, that is, $$V_L\mathcal{A} = \Lambda V_L\\ \mathcal{A}V_R = V_R\Lambda\\ V_LV_R = I_{k\times k}$$ $V_L$ being the $k\times N$ ...
Nikko's user avatar
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401 views

How to reuse permutation-orderings within scipy's SuperLU-wrapper?

i'm solving sparse linear equations within scipy 0.18 which internally resorts to SuperLU (after umfpack got removed due to license-issues). Current, i'm doing a complete re-factorization in each ...
sascha's user avatar
  • 131
3 votes
0 answers
697 views

Gradients of non-uniformly sampled data in 3D space

I have measurements of magnetic field on a 3d grid. My measurements are distributed on four x-y planes similar to what is shown in the image below. The measurements roughly follow a Cartesian grid but ...
jensv's user avatar
  • 133
3 votes
0 answers
2k views

BFGS Fails to Converge

The model I'm working on is a multinomial logit choice model. It's a very specific dataset so other existing MNLogit libraries don't fit with my data. So basically, it's a very complex function ...
Titanic's user avatar
  • 131
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 ...
Strichcoder's user avatar
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 \...
Klaus3's user avatar
  • 133
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 ...
Xun Maoapo's user avatar
2 votes
0 answers
266 views

Providing Jacobian as LinearOperator in scipy.optimize.root

I asked this question a few days ago on stackoverflow, but I figure scicomp.stackexchange is probably a better place. Sorry for the double post. I want to solve a system of nonlinear equations using ...
G. Fougeron's user avatar
2 votes
0 answers
37 views

Scaling tensor approximation by symmetric tensor decomposition with SciPy's L-BFGS-B

I am trying to approximate a symmetric tensor of which the values are in the range of [1e-7,1e-4], by a symmetric tensor decomposition of lower rank. For this I am using the L-BFGS-B method in SciPy's ...
Jules's user avatar
  • 21
2 votes
0 answers
161 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^...
tBuLi's user avatar
  • 121
2 votes
0 answers
99 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 ...
arandoperson's user avatar
2 votes
0 answers
2k views

Solve system of polynomial equations with Python

I have 5 at most 4th order polynomials in 5 variables, $$p_i(x_1,x_2,x_3,x_4,x_5) \qquad i = 1, \ldots, 5$$ where all coefficients are either rational or floating point. I'd would like to get the ...
Fetchinson0234's user avatar
2 votes
0 answers
761 views

finding null space to a complex matrix

I need to solve the following equation: $$ \begin{pmatrix} \frac{\omega^2}{c^2}\varepsilon_x-\mu_z^{-1}k_y^2-\mu_y^{-1}k_z^2 & \mu_z^{-1}k_xk_y & \mu_y^{-1}k_xk_z\\ \mu_z^{-1}k_xk_y &\...
Physicist's user avatar
  • 217
1 vote
0 answers
254 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
1 vote
0 answers
287 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
104 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
  • 433
1 vote
0 answers
3k 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
0 answers
394 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
1 vote
0 answers
113 views

How do you correctly implement Scipy's FFT procedures to produce a low-pass filter - image processing

I'm following this low-pass filter example in the text "Image Operators: Image Processing in Python 1st Edition" by Jason M. Kinser, but can't seem to duplicate their results. The text's ...
Lagreeni's user avatar
1 vote
0 answers
54 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 ...
Smilia's user avatar
  • 468
1 vote
0 answers
382 views

Rank filter on an nXm array using python

I would like to apply a rank filter on an nXm numpy array. Let's say I have this array: ...
user88484's user avatar
  • 121
1 vote
0 answers
60 views

Update model parameter with new data, discarding old data

I have this dataset, and I am using y = (a * x^n) / (b + x^n) Hill function as the model, where a is the limit of the Hill curve,...
neo4k's user avatar
  • 11
1 vote
0 answers
468 views

Numerical integral of oscillating function with known zeros

I have a function that I need to numerically integrate from $0$ to $+\infty$, given by: $$I = \int_0^{+\infty} \mathrm{d}x\,x\,T^2(x)f(x)$$ where $T^2$ is an interpolated function that goes to $1$ ...
HR_8938's user avatar
  • 111
1 vote
0 answers
113 views

solving numerically a 2D integral by using simps and quad combined

I have the following function $$f(x,y) =\left(\frac{1}{\exp(x-E_f)+1}-\frac{1}{\exp(x-y-E_f)+1} \right)\frac{1}{\sqrt{4-xy}}$$ I want to integrate it using Python 3. The domain of the $y$ variable ...
Small Pole's user avatar
1 vote
0 answers
871 views

Numerical Double integration with endpoint singularity in scipy Python gives incorrect answer

I am trying to integrate the following function in Python, $\int_{0}^{\infty}\int_{0}^{\infty} \dfrac{e^{-x-y}}{B(x,y)}dx dy$, where $B(x,y)$ is the beta function - $B(x,y) = \int_0^{1}a^{x-1}(1-a)^{...
Siddhartha Satpathi's user avatar
1 vote
0 answers
81 views

Convert scipy integration with one step to matlab integration

Scipy integration allows us to do ode integration one adaptive timestep at a time and do something to it. However, matlab ode needs us to specify a timespan , and determine the adaptive timestep ...
diff's user avatar
  • 121
1 vote
0 answers
348 views

Vectorize function integration

I need to implement the following in python: For a given discrete time series $Z_t$ ($t={0...T}$), find the smallest $t$ such that: $$c\sum_{s=0}^t e^{[k(Z_t-Z_s)+m(t-s)]} \geq \frac{p^*}{1-p^*} $$ ...
dayum's user avatar
  • 163
1 vote
0 answers
1k views

linearly interpolate and determine gradients for data on non-uniform grid

I have measurements of a quantity on a 3d grid. My measurements are distributed on four x-y planes similar to what is shown in the image below. The measurements roughly follow a Cartesian grid but ...
jensv's user avatar
  • 133
1 vote
0 answers
191 views

Generalized Hermite Function as eigenfunction of a differential operator

I'm going through this paper. The article defines function function $\phi_n^\mu(x)$ that is orthonormal on $L^2$ with measure $dm = dx$: \begin{equation} \phi^\mu_n =\left(\frac{\gamma_\mu(n)}{\...
Константин Высоцкий's user avatar
1 vote
0 answers
196 views

Is it worth switching to timesteppers provided by PETSc if I can't write down a Jacobian for my problem? Case study with "the amoeba" toy problem

I am considering using petsc4py instead of scipy.integrate.odeint (which is a wrapper for Fortran solvers) for a problem ...
bzm3r's user avatar
  • 659
1 vote
0 answers
192 views

How to compute frank copula and its derivative accurately?

I need to fit a model using MLE with Frank copula by linking two discrete univate distribution function $u = F(x)$ and $v = F(y)$ together, and the joint distribution function is $$ \Phi(x,y) = C(F(x)...
wh0's user avatar
  • 183
0 votes
0 answers
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 ...
Manuel Borra's user avatar
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 ...
Joao Victor Ferreira da Costa's user avatar
0 votes
0 answers
36 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 ...
Lorenzo Carfora's user avatar
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 ...
Rubens Filho's user avatar
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 ...
blov's user avatar
  • 43
0 votes
0 answers
140 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 ...
HWIK's user avatar
  • 23