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Questions tagged [python]

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

7
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0answers
54 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 ...
4
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0answers
161 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
423 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
221 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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0answers
127 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
83 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
143 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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0answers
208 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
85 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
288 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
917 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
911 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
154 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
91 views

Computing the structure factor from positions and radial distribution function

I'm currently analysing some spatial point patterns that come from some fluid dynamics simulations and I'm having some difficulty computing the structure factor, $S(\pmb{k})$, from both the positions ...
2
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0answers
93 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
89 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
146 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
183 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
779 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
202 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
150 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
154 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
votes
0answers
303 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
311 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
votes
0answers
298 views

Return derivative vector from odeint scipy function

I have the following function that I want to implement in scipy.integrate.odeint ...
2
votes
0answers
585 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
votes
0answers
349 views

My calculated laser pulse duration is too large. Where am I wrong?

I am currently writing a small Python script to estimate the pulse duration from the optical spectrum. At the end, the idea is to observe the effects of the spectral phase on the pulse duration and ...
2
votes
0answers
623 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
315 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
926 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 ...
1
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0answers
37 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 ...
1
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0answers
45 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 ...
1
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0answers
29 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 ...
1
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0answers
75 views

SDE solver in python: manual determination of integrator step size (dt)

Aim: I am trying to solve a system of SDEs, while using the SDEint package in python 3.x. It is a system of SDEs adapted from and inspired by the Zombie Apocalypse ...
1
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0answers
154 views

Speeding up the solution of a large set of nonlinear algebraic equations in `sympy`

I have a quite large algebraic equation system to solve, the system is so large, I can't post the example here, so I am posting it to pastebin. The sympy.solve is ...
1
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0answers
71 views

How to compute large condition number of a matrix in Python?

I have a matrix that is extremely singular, but I am still interested in computing the exact condition number, which is the ratio between the largest and smallest singular values. Is it possible to ...
1
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0answers
383 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 ...
1
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0answers
168 views

Use of Morton Key to reduce number of grid points

I asked a question on Stack Overflow Performance Issue with VP Trees and Nearest Neighborsand I was not satisfied with the answer and so I thought I would reword my question for this site and post ...
1
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0answers
350 views

Which solvers for BVP in python are the best? Is there something better that scipy.integrate.solve_bvp?

I am trying to solve a boundary value problem with Python. I have been using scipy.integrate.solve_bvp but the result that it is giving me is completely wrong. Basically my code is as follows: ...
1
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0answers
80 views

computing dual matrix trace norm and tensor gradient in python

I'm trying to write the following function in python: $$ f_\mu(\mathcal X) = f_0(\mathcal X) + \sum_{i = 1}^n \max_{||\mathcal Y_{i(i)}|| \leq1} \alpha_i\langle \mathcal X_{(i)},\mathcal Y_{i(i)} \...
1
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0answers
81 views

Global truncation error behavior at fixed time step

I am trying to solve the following diffusion equation problem: $\frac{\partial f}{\partial t}=\frac{\partial (D\frac{\partial f}{\partial x})}{\partial x}+S$ $D=1+x^{2}+\sin(x)$ $f(x,0)=1 , f(0,t)...
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0answers
137 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: ...
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0answers
936 views

Software for easy spherical coordinate plotting from data file

Does anyone have any suggestions for good open source plotting software which has good graphical spherical coordinate plotting (from a data file). I have a three column data file where column 1 is $\...
1
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0answers
122 views

Finding integer/lattice points (coordinates) inside a polytope/polyhedra?

I am using Python but I wouldn't mind changing language. All I have gotten from my research are tools to count the number of (lattice) points inside a region given the equations for the planes that ...
1
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0answers
221 views

Vectorised root finding in Python

I have an array of size (254, 80) which I am trying to use Scipy's fsolve on. I have found that the speed of using fsolve on a vector is quicker than it is in a for loop but only for vectors upto ...
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0answers
107 views

FiPy with derivative source terms

I have a coupled nonlinear PDE system in 1 spatial dimension, in which I want to solve using FiPy. The dependent variables are $n$ and $T$: \begin{align} \frac{\partial n}{\partial t} \,&=\, D\,\...
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0answers
47 views

Python package to calculate static force and moments of rigid body

Which Python package is suited for solving problems of the following type? Given the rigid body depicted in violet in the following sketch I would like to do the following: Define cartesian ...