# Questions tagged [python]

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

442 questions
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### Determining the pseudo-time period of a system of $n$-pendulums via Kane's method in Python

We can use Kane's method to integrate the equations of motion for a system of $n$ pendulums with arbitrary masses and lengths (see derivation). In particular, if $(x_i,y_i)$ denotes the Cartesian ...
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### Poincare map for Arnold-Beltrami-Childress Magnetic Field in Python

I want to plot the Poincare map for Arnold-Beltrami-Childress magnetic field for parameters $A=1, B=0.816, C=0.5773$ in Python for the Poincare section $z=0$. Also, I am not able to understand what ...
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### Use data from VRML 2.0 UTF-8 file to make a 3D representation of object with mplot3d

I have a VRML file with three types of data, points; normal-vectors; coordIndex. I have successfully, using re, imported the data into Python. I thought I had a way of using this data to make a nice ...
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### Python implementations of Gillespie's direct method

I'm looking for a decent implementation of Gillespie's Direct Method in Python, as if I code the algorithm myself I'm nigh positive I'll do it inefficiently. Anyone have a favorite?
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### Minimum path on known potential surface

I'm searching for the minimum path between the minima of a potential surface that is already known on a grid. (source: http://www.math.nus.edu.sg/~matrw/string/) Any point on the path is at an ...
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### Python Finite Difference Schemes for 1D Heat Equation: How to express for loop using numpy expression

Hello all, I've recently been introduced to Python and Numpy, and am still a beginner in applying it for numerical methods. I've been performing simple 1D diffusion computations. I suppose my ...
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### Efficiently generate a random subgraph (Gs) with maximum degree K, using only edges from an existing graph G

I am looking find a way of efficiently generating a random, undirected subgraph $G_s$ with $N$ vertices, using a subset of edges from an exisiting undirected graph $G$, also of size $N$, where the ...
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### Solve 3-D Heat equation with Neumann boundaries

I want to solve the Poisson PDE for heat flow in a 3-D solid cube with given dimensions $x$, $y$, and $z$: $$\rho C\frac{\partial T}{\partial t} = k \Delta T$$ The cube is irradiated with a constant ...
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### Interatomic distance-periodic boundary conditions-non cubic unit cell

I am trying to find interatomic distance considering periodic boundary conditions for hexagon cubic cells (graphite). I tried to follow the answers to these two questions here but am unable to get the ...
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### Recommended language/environment for large scale semi-continuous biological models

We have a fairly large (maybe 1000 equations) differential-algebraic equation model written in ACSLX, an obsolete modelling environment similar to Modelica. The model represents the evolution of a ...
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### fmincg implementation in Python

I'm trying to re-implement Neural Networks in Python. I implemented the cost function and the backpropagation algorithm correctly. I have checked them by executing its Octave equivalent code. But ...
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### 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 ...
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### Calculate partial trace of an outer product in Python?

I have a python implementation of calculating the partial trace over select dimensions. ...
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### Showing date in Paraview's Annotate Time Filter

I have a time dependent data set where each frame corresponds to a certain date. I need to show the time annotation, much like what Annotate Time Filter does, but show the date instead of time as a ...
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### Why does Matlab's integral outperform integrate.quad in Scipy?

I am experiencing some frustration over the way matlab handles numerical integration vs. Scipy. I observe the following differences in my test code below: Matlab's version runs on average 24 times ...
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### Python - Fitting a function to data without using Scipy

I'm trying to write a program in python which doesn't need to use extra packages like numpy and scipy. In one part of the project, if I can interpolate a function to a set of data, I can save ...
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### Using gmsh python api for meshing a model with grouping elements by their volumes and surfaces

I am trying to use GMSH python api for creating 2d meshes of cad formats. I managed to write a script that can generate mesh successfully. However I need to know how elements are separated across ...
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### Are there any “light-weight” FEM packages around?

Basically, FEM seems to be a problem that is pretty much "solved". There are numerous powerful frameworks existing, like Trilinos, PETSc, FEniCS, Libmesh or MOOSE. One thing they have in common: They ...
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### 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 $1/(1 + \exp\left(\sqrt{S}(x-x_c)\right)$...
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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 ...
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### Probability of reconstructing a word using c substrings from a random sample

Consider a voice recording split into it's phonemes as our sample $S=(s_1,...,s_k) \in \Omega = P^k$. The number of phonemes is $|P| = 40$. Then I have a word $w = (w_1,...,w_n) \in P^n$. I want to ...
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### Solving a least squares problem with linear constraints in Python

I need to solve \begin{alignat}{1} & \min_{x}\|Ax - b\|^2_{2}, \\ \mathrm{s.t.} & \quad\sum_{i}x_{i} = 1, \\ & \quad x_{i} \geq 0, \quad \forall{i}. \end{alignat} I think it is a ...
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### why am I not getting a staircase for the rotation number?

I'm trying to understand the staircase map. Look at this map from the circle to itself: $$x \stackrel{F}{\mapsto} \big[\omega + x + \tfrac{\epsilon}{2\pi} \sin (2\pi x) \big] \pmod 1$$ Such a map ...