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Questions tagged [python]

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

4
votes
1answer
3k views

Python Vectorizing a Function Returning an Array

I have the following function that has been vectorized so that for every element in input array t, an array is output: ...
1
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0answers
59 views

Solving a nonlinear problem with CDF

I'm trying to solve this problem: $\begin{cases} \partial_t E=-k\left([f(\rho)-i.\left[\delta+\frac{1}{2}a\left[\dfrac{\nabla^2_{\bot}}{4}+1-\rho^2\right]\right]]E - 2CP\right)\\ \partial_t P=-\...
5
votes
2answers
102 views

How to read the number of periods of this complicated graph?

I have two data sets that are quasi-periodic. They have the same period and can be seen clearly by eye. For example when $x\in(100,200)$, both of them have about 32 periods. Below is a zoom-in of the ...
1
vote
1answer
37 views

How to use compiled python packages for matrix initialization

Assume I have an expression for an matrix initialization, for example the following: A[i,i-2*j+k] = B[i-k] * C[i] * D[i+j+k] In order to execute such a process, I could loop over all i, j and k. ...
0
votes
1answer
684 views

Finite-difference approximation of the 2nd derivative operator matrix for a staggered grid

I'm working on a computational physics assignment and I was looking for some help as I've got stuck! The question is: Write a function to create the finite-difference approximation of the 2nd ...
2
votes
0answers
152 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 ...
1
vote
2answers
3k views

Multiple Coupled Differential Equation solution in Python

I have 4 ordinary differential equations that are coupled. The variables in the 4 equations are functions of time and space and one of them is second order in space. \begin{equation} \frac{ \partial ...
1
vote
1answer
765 views

Heat Equation - PDE

I'm trying to model the Black-Scholes Equation (transformed into a heat equation) using method of lines in Python. The transformed formula is basically \begin{equation*} \frac{\partial u}{\partial ...
1
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0answers
166 views

Inverse quadratic method only makes one iteration - python

I'm tryin' to implement this method with python3 but i don't solve the problem. This is my code: ...
3
votes
2answers
193 views

How to separate text from the paper on a black and white page?

I tried to discretize an image into black and white and came into some difficult. The difference between the letters and paper is pretty clear to our eyes: However a simple thresholding trick doesn'...
0
votes
2answers
501 views

Wave Equation PDE [closed]

I'm trying to solve the following PDE wave equation using method of lines: Wave Equation: u_tt = u_xx with initial condition: u(0,x) = sin*pi,u_t(0,x)=0, 0 < x < 1 boundary ...
3
votes
2answers
845 views

Hyperbolic Equation PDE (Python)

I'm trying to solve the following first order hyperbolic PDE problem using method of lines: Hyperbolic Equation: $u_t = -u_x$ with initial condition: $u(0,x) = 0, 0 < x < 1$ ...
1
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0answers
83 views

Need suggestions on how to implement this time stepping for wave equation

I have the following system of equations obtained by implementing Sympletic Euler time scheme to wave equation. I want to model this in Fenics. Here 'u' is the displacement and 'p' is corresponding ...
4
votes
3answers
8k views

LCM builtin in Python / Numpy

I can write a function to find LCM (lowest common multiple) of an array of integers, but I thought it must have been implemented in numpy or scipy and was expecting something like ...
0
votes
1answer
308 views

Variational Monte Carlo: Variational energy is lower than ground state energy

I'm writing a VMC simulation for hydrogen and helium atoms, but in both my codes my variational energy for certain wavefunctions is not only statistically different from my expectation value, but it ...
1
vote
1answer
54 views

Calculate proportions of exponentially weighted factors avoiding underflow problem

I am trying to implement in Python this ratio: $\frac{w_t(i)}{\sum w_t(j)}$ where $w_t(i) = w_{t-1}(i)\cdot\exp{(-x_{t}(i))}$, i.e. the weights are exponentially decreasing without running into ...
2
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0answers
282 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) =...
6
votes
1answer
1k views

Numerical solution of Geodesic differential equations with Python

I have made a solver based on the SymPy.diffgeom library, where I use Scipy.Integrate to solve the following system of second order differential equations : \begin{align} u'' &+ \Gamma^0_{00}(u')...
1
vote
2answers
103 views

Heat Equation Solution in One Dimension (x, t)

We're currently solving the heat equation as a part of the PDE sequence in class. We've been given the formula:$$T(i, n+1) = T(i,n)+\alpha \left [\frac{T(i+1,n)-2 T(i, n)+T(i-1,n)}{\Delta x^2} \right ...
1
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0answers
497 views

best package choice for visualizing agent based model simulations in python

This is a visualization/programming design problem. I am working on building a geospatial agent based model, meaning that there are multiple agents interacting within some particular spatial container....
2
votes
3answers
2k views

Runge-Kutta Simulation For Projectile Motion With Drag

I am attempting to simulate projectile flight with drag. However, with a timestep of 0.1 seconds, I am consistently getting an error of ~0.1-1%. ...
1
vote
1answer
381 views

Diffusion with space dependent drift in Fipy

I need to solve a diffusion equation in periodic boundary conditions using fipy but I would like to have a drift term that depends on the position so like this: $$ \partial_t u(x,t) = \partial_x^2 u(x,...
0
votes
1answer
171 views

Solve a pair of coupled nonlinear equations within certain limits

This answer to this question works only for situations in which the desired solution to the coupled functions is not restricted to a certain range. But what if, for example, we wanted a solution such ...
1
vote
1answer
234 views

Python package for large absolute value optimisation

I have an absolute value optimisation problem $$\min_x \sum |r-Cx|$$ where $x$ is small around 200 dimension. But $C$ has lots of rows, $C_{30000\times200}$ and $r$ is $30000\times1$. So this will ...
2
votes
0answers
285 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 ...
8
votes
1answer
900 views

Test of 3rd-order vs 4th-order symplectic integrator with strange result

In my answer to a question on MSE regarding a 2D Hamiltonian physics simulation, I have suggested using a higher-order symplectic integrator. Then I thought it might be a good idea to demonstrate the ...
1
vote
1answer
119 views

Computation of plane wave scattering on semi infinite plane

I have attempted to code up the simple math required to plot the total field set up by an incident plane wave on a semi-infinite flat plate which can be found here. To summarise: $$\phi_s(r,\theta ) ...
1
vote
0answers
591 views

How to adjust scikit-learn FactorAnalysis() settings to get scores output similar to one from factanal() in R?

I'm new to factor analysis and I need to compute factor scores using Python. I have R code to compute scores and I want to ...
5
votes
1answer
1k views

Alternatives to numpy.einsum

Given an $n_1 \times \cdots \times n_k \times g \times g$ tensor $A$ (i.e. a collection of $g \times g$ matrices) and an $n_1 \times \cdots \times n_k \times g$ tensor $b$ (i.e. a collection of ...
2
votes
1answer
361 views

How to convert MPIAIJ to SEQAIJ matrix in petsc/petsc4py?

I am curious, if there is a function to convert MPIAIJ (distributed matrices in AIJ format) to a SEQAIJ matrix that lie on a single processor. It is possible to do such an operation for PETSc vectors ...
3
votes
1answer
923 views

How can I solve wave equation for circular membrane in polar coordinates?

The original equation is $$\frac{1}{c^2} \frac{\partial^2 u}{\partial t^2} = \frac{\partial^2 u}{\partial r^2} + \frac{1}{r}\frac{\partial u}{\partial r} + \frac{1}{r^2}\frac{\partial^2 u}{\partial \...
1
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0answers
176 views

Differences in answers between Python and Fortran [closed]

I am translating a piece of Fortran code into Python and am testing my code with a certain test case. All the results differ with 0.04% compared to the Fortran results. This is a very small ...
3
votes
2answers
1k views

Scipy OdeInt solver with Neumann boundary conditions

I'm using scipy.odeint to solve Fisher-Kolmogorov equation: \begin{equation} u_t = u_{xx}+u(1-u) \end{equation} The code can be found here. From Ablowitz and ...
2
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0answers
245 views

Return derivative vector from odeint scipy function

I have the following function that I want to implement in scipy.integrate.odeint ...
3
votes
1answer
528 views

Simple Runge-Kutta Scheme for nonlinear PDE

I am new to this community as well as to scientific programming. I programmed a simple 4th order Runge-Kutta for the 1-D Cahn-Hilliard Equation for some first simple calculations on pattern forming ...
5
votes
1answer
232 views

Iterative Cunnigham correction in Millikans oil-drop experiment

I tried to write an analysis program in python for the Millikan experiment based on a paper from Jones "The Millikan oil‐drop experiment: Making it worthwhile" However, I cannot reproduce the ...
2
votes
0answers
502 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
302 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 ...
1
vote
1answer
2k views

Implementation of 1D Advection in Python using WENO and ENO schemes [closed]

I'm trying to implement 1D advection solver using WENO and ENO schemes. \begin{equation} \frac{\partial u}{\partial t} + \frac{\partial f(u)}{\partial x} =0 \end{equation} where: \begin{...
6
votes
2answers
4k views

Solve non-linear set of three equations using scipy

I need to solve a non-linear set of three equations using scipy. However, I do not have any clue on which algorithm is suitable for my problem from a mathematical point of view (stability, ...
1
vote
1answer
573 views

Convert Image of Map to 2D Grid in Python

I have this map showing the geography of Europe (below), and I wish to convert it to a matrix in python that would be a 2D approximation of this image where 0's would represent the ocean and 1's would ...
1
vote
1answer
514 views

Improper Numerical integral

I am self teaching myself python and computational physics via Mark Newmans book Computational Physics the exercise is 5.17 of Computational Physics. I have to shift the limits of integration for an ...
5
votes
2answers
5k views

Python solvers for mixed-integer nonlinear constrained optimization

I want to minimize a black box function $f(x)$, which takes a 8$\times$3 matrix of non-negative integers as input. Each row specifies a variable, whereas each column specifies a certain time period so ...
7
votes
1answer
459 views

Python trust region optimization code that allows ellipsoid-shaped trust regions

Are there any high quality trust region optimization implementations that allow nonspherical ellipsoid trust regions, and are written in Python, or are easy to call from python? By nonspherical ...
1
vote
0answers
46 views

Execute commands when starting ipdb [closed]

I usually debug a python script by putting the following line into the source code: import ipdb; ipdb.set_trace() Then when I run the script, ipdb starts. Very ...
2
votes
0answers
552 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\...
1
vote
4answers
2k views

Computing the Madelung constant

I am self teaching myself python and computational physics via Mark Newmans book Computational Physics the exercise is 2.9 of Computational Physics I have to compute the Madelung constant. . I have ...
4
votes
0answers
398 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 ...
1
vote
2answers
2k views

How to use the basic Sparse matrix operations (multiplication, .etc) in PyCUDA

I try to use sparse matrix operations in GPU in Python and now try to use PyCUDA with theano. But I can't find how to do sparse matrix and vector multiplication. I only got an example showing how to ...
1
vote
0answers
395 views

scipy.integrate.ode ignores boundary conditions

I am trying to solve the 1-dimensional diffusion problem numerically using method of lines: $$ \frac{\partial c}{\partial t} =D \frac{\partial^2 c}{\partial z^2},$$ where the right hand side is ...