Questions tagged [python]

A general purpose high-level programming language that emphasizes ease of code syntax and readability.

113 questions with no upvoted or accepted answers
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74 views

How reproducible are conda environments?

I am aiming at keeping my scientific studies and analyses reproducible: I am automating them as much as possible, I am sharing them, and I sharing them together with the execution environment(s) I've ...
6
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99 views

fastest way to compute many small dot products

I have two n-by-3 blocks contiguous in memory ("n vectors of length 3") and I'd like to compute the dot product between each of the rows as fast as possible. In numpy, using ...
5
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0answers
31 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 ...
5
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0answers
31 views

Implementation of Lanczos method that returns tridiagonal matrix

The Lanczos method can be used to obtain extremal eigenpairs of sparse symmetric or hermitian matrices. I know there are several implementations of the Lanczos method (as well as Arnoldi, Davidson, ...
4
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0answers
234 views

Solving a PDE implicitly by iteration in python

Connected to this question here on Computational Science, I've posted a follow-up question on how to solve a PDE using an implicit scheme like Crank-Nicholson in general in this question on SO. But I ...
4
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0answers
454 views

Large meshing with tetgen

So I have a point cloud that I am creating a 3D flat rectangular surface from. I'm then turning it into a hollow box and connecting the corners by just dropping this surface mesh down. I need it to ...
4
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0answers
1k views

Python - calculation time derivative and laplacien by finite differences

I would like to determine a temporal derivative and a Laplacian by the finite differences method to solve the heat equation in a 1-dimensional case. My aim is to get the sources term that is why I ...
4
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0answers
226 views

Negative viscosity stabilized by fourth order terms

I am trying to solve a "Navier-Stokes"-type problem where the viscosity is negative. Of course this renders the equation unstable and thus I add a fourth order term, so the entire equation becomes: $$...
3
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1answer
85 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 - \...
3
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0answers
163 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\...
3
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0answers
84 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) $...
3
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0answers
188 views

Avoiding divergent solutions with `odeint`? shooting method

I am trying to solve an equation in Python. Basically what I want to do is to solve the equation: $$ \frac{1}{x^2}\frac{d}{dx}\left(Gam \frac{dL}{dx}\right)+L\left(\frac{a^2x^2}{Gam}-m^2\right)=0 $$ ...
3
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1answer
560 views

Numerical Sensitivity in Density of States of Tight-binding model

I'm working with the tight-binding model, and I'm trying to learn the basics of how to compute the Density of States (DOS) $N(E)$ numerically. The DOS is given by $$N(E) = \frac{1}{N}\sum_k \delta(...
3
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258 views

Open source implementation of Multiscale Combinatorial Grouping

I would like to use Multiscale Combinatorial Grouping for my PhD research. However, I am restricted to use open-source implementations and this one runs on Matlab. Does anyone know of an equivalent ...
3
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0answers
87 views

How to optimize for decay constant in exponential-like function?

I've got a data set of points $M_O .. M_N$ for time points $t_0 .. t_N$, where $N$ is approximately 10-20, and the spacing of time is not uniform (i.e., $t_{i+1}-t_i$ is not constant for all i). It is ...
3
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0answers
1k views

Efficiently creating an adjacency matrix from a lattice in numpy

I have an $n$ by $m$ numpy array representing a rectangular lattice $L$, where each site contains a one or a zero, representing two different materials. I'm modelling heat flow across this lattice. ...
3
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0answers
307 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{...
3
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0answers
987 views

Polynomial Fitting with Least Squares using Numpy and Scipy

I am trying to fit data to a polynomial using Python - Numpy. The points, with lines sketched above them are as in the picture. I am trying to fit those points to a polynomial of 4. or 5. degree. ...
3
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0answers
1k 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 ...
3
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0answers
157 views

Is there an easy way to read a PetscBag into a python dict?

I'm using a PetscBag to store the input parameters of my program. At some point, I'm going to need to use python to plot these parameters against some output parameters, and ...
2
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0answers
92 views

Heisenberg Model python : Specific heat capacity for spin 2

I have the correct plot for specific heat capacity when I am using the formula which is $C_V$ = differentiation of entropy with respect to temperature. However, When I try to calculate $C_V$, by using ...
2
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0answers
53 views

Efficient algorithm to determine the intersection volume of simple convex polyhedra

TLDR: Is there an efficient algorithm to compute the intersection of polyhedra with 8 or fewer vertices? I have two sets of FEM meshes for one geometry (one exhibiting a skin effect). I have to ...
2
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1answer
109 views

Incorporating a potential barrier in a wave-packet simulation (Fourier Transform method)

I'm trying to simulate the scattering of a wave-packet at a potential barrier in Python. I'm using a Fourier Transform method (not sure if its the same as the Split-Step method), where I apply Fourier ...
2
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0answers
116 views

2D reaction-diffusion system simulation

I am a complete beginner in numerical simulation and I am pretty lost about how to tackle this problem. I have been trying for some time to find the steady state (or simulate), the following system ...
2
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0answers
91 views

Precision not improving by decreasing step-size in nonlinear Schrödinger

I tried to simulate soliton propagation by solving the nonlinear Schrödinger equation using the split-step Fourier method. The following is an example of the Matlab code copied from a textbook. ...
2
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0answers
167 views

Optimizing for loops by using Einstein summations instead

I have some Python code containing a couple of for loops, which I would like to optimize by using low-level functions. My first approach is to use ...
2
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0answers
216 views

minimalistic library for classical molecular mechanics force-field in C/C++/Python

I would like some classical molecular mechanics forcefield library or super-simple program which does not have any external dependences, so that I can plug it into my software without worry of "...
2
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0answers
970 views

Using RK2 Method to solve the simple harmonic oscillator of a horizontal mass on a spring (1D)

Being new to numerical analysis techniques, in particular RK2, I decided the best way to jump in is by using python to solve the well known mass-spring oscillator using RK2 techniques. My problem is ...
2
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0answers
217 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 ...
2
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0answers
120 views

Clustering similar words and mapping to numbers in Python

I'm familiar with kmeans to cluster data points, but not text.. So I have one column of words in cvs format, which I want to cluster those which have similar word or more, and then mapping those ...
2
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0answers
166 views

scipy.linalg.sparse.eigsh does not work for generalised eigenvalues

I asked this question over at StackOverflow and someone told me that I'd get a better answer here. So here's my problem: I'm working on a machine learning project which involves doing a Principal ...
2
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0answers
161 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 ...
2
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0answers
331 views

Solving constrained BVP, singular Jacobian

The boundary value problem is $$ \begin{cases} \dot{x}_i = \begin{cases} (0.5D^{-1}\psi)_i, \text{ if }(0.5D^{-1}\psi)_i \le 0 \\ 0 \text{, otherwise} \end{cases} \\ \dot{\psi} = 2\Sigma x \\ x(0) =...
2
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0answers
328 views

Adaptive Finite Element Method - Laplace

I'm currently attempting to turn my code for solving the laplace equation using finite element approximations into an adaptive one using the dual weighted residual as my error estimator: i.e. my ...
2
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0answers
342 views

Return derivative vector from odeint scipy function

I have the following function that I want to implement in scipy.integrate.odeint ...
2
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0answers
638 views

Solving a system of 4 coupled PDEs representing variable diffusivity

I have four partial differential equations representing mass conservation of two compressible fluid phases (marked by subscripts $p1$ and $p2$) in two different continuum media (marked by subscripts $...
2
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0answers
655 views

Precession of Mercury Python simulation

I was trying to simulate the precession of Mercury based on the perturbed solution: $$\frac{1}{r}=\frac{m}{B^{2}}(1+e\cos\phi+3\frac{m^{2}}{B^{2}}(1+e\phi \sin\phi +e^{2}(\frac{1}{2}-\frac{1}{6}\cos2\...
2
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0answers
327 views

Stationary 2D/3D Navier-Stokes source code

Trying to solve stationary Navier-Stokes problem for incompressible laminar Newtonian fluid. I've found a couple solutions for instationary Navier-Stokes equations (like FeniCS examples or CFD Python)...
2
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0answers
950 views

Newton Iteration method convergence

I wrote a Python code which solves a second degree nonlinear differential equation using the Newton iteration method. The code converges to a 2-cycle within 50 or so iterations. The cycle only ...
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0answers
67 views

Runge-Kutta for PID and system in separate calculations without filter

I need to calculate a closed-loop system in Python; specifically, obtain the PID response and then use the output to obtain the system response sample-by-sample with my own loop. For this, I am ...
1
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0answers
70 views

How to translate Python infinitely big integer into Cython?

I want to factorize very huge numbers (e.g. 100-bits, 200-bits numbers) with Cython. Hi everyone, I implemented the Elliptic Curve Method for factorization into Python 3.6. Now, I want to speed up my ...
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0answers
16 views

Find all recurring subgraphs/patterns of maximal size in a single undirected, labeled, connected graph

I would like to identify all subgraphs of maximal size (maximum number of nodes) that are recurrent in a single undirected, labeled, connected graph. I provide exemples of input and expected output ...
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0answers
78 views

How to perform local sensitivity analysis for partial differential equations

I am looking for a way to do local sensitivity analysis for PDEs, preferably in Python. I get the impression that discretizing the equation then treating it as an ODE could work; however, would that ...
1
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1answer
46 views

Draw contour line to represent multiple contours

I have 5 data sets, each includes multiple scatter points. If I use the geom_path function in R, I could obtain 5 contours like the following graph shows. Those five contours are annotated outlines ...
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0answers
54 views

How to get the derivatives of the determinant and inverse of 2nd-order tensor wrt itself in SymPy?

I have a second-order tensor for which I need to compute the derivatives of its determinant and inverse w.r.t. itself. The equations are as follows: $$\frac{\partial \, det(\mathbf{F})}{\partial F_{...
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0answers
74 views

Solved : Damped spring-mass system, wrong position, correct speed and acceleration

I am modulating a spring-mass system with gravitation and aero drag, with python programming. The spring is hanging vertically and attached a weight. The user then selects a length to drag it down ...
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0answers
63 views

How to use Wolfe-Powell step-size control in quasi-Newton method?

I'm trying to find the minimum of a function using the quasi-Newton method with the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. But I want to change the following implementation, so that: 1) ...
1
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0answers
44 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 ...
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0answers
51 views

Numerically Approximating the Jacobian and Comparing the Eigenvalues With Analytical Form

I am trying to study the stability of numerical discretization schemes using the Jacobian matrix of the residues with respect to the vector of conserved variables. For a simple diffusion equation ...
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0answers
31 views

Why does the correlation function of this stochastic differential equation starts at different points?

I am working with the following differential equation: The equation is $$x=\beta +\sqrt{2D} \xi(t)$$ where $\xi(t)$ is a white noise term, with a reflecting wall boundary conditions. After solving ...