Computational Science Stack Exchange
Computational Science Stack Exchange

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1500 questions
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2 answers

Python package for (adaptive) function plotting

Are there any mature Python packages that can plot functions, and possibly use adaptive sampling? I am looking to pass only a function (can be a numerical black box) and a range, and expect a plot as the output. What I am not looking for: manually…
Szabolcs
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Is multigrid useful for finding all eigenvalues and eigenvectors of a differential equation, or only the lowest eigenvalues?

I've been considering using a multigrid method to calculate the eigenvalues of a particular PDE. I know that multigrid is extremely good at finding the least eigenvalues and their associated eigenvectors, in part because these eigenvectors are very…
Dan
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4 answers

Should I use a database to handle large amounts of results?

Background: I am currently running a large amount parameter variation experiments. They are being run in Python 2.6+, using numpy. These experiments are going to take about 2 weeks to run. Roughly I am varying 3 parameters (independent variables)…
Frames Catherine White
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How can I seed a parallel linear congruential pseudo-random number generator for maximal period?

Normally when I seed a sequential random number generator in C, I use the call srand(time(NULL)) then use rand() mod N to obtain a random integer between 0 and N-1. However, when I do this in parallel, the calls to time(NULL) are so close to…
Paul
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Where to find data sets for testing minimum vertex cover algorithm for bipartite graphs?

I'm playing with simple implementations of algorithms to find minimum vertex cover/maximum cardinality matching in bipartite graphs. However, I seem to have trouble googling for some test data sets that I could use to verify, if I got that one…
Piotr Kalinowski
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4 answers

High Order derivatives of splines using SciPy

I have created a spline to fit my data in python using: spline=scipy.interpolate.UnivariateSpline(energy, fpp, k=4) The equation I want to use involves a summation between n=2 and n=infinity, where n is the order of the differential at a point Eo.…
Karim Sutton
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4 answers

Are open-source codes available to study protein folding?

I would like to test the influence of solvation parameters in implicit solvation models and wonder which codes are freely available as standalone programs for protein folding of small proteins, and which use energy minimization approaches instead of…
Open the way
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Adaptive mesh refinement with perfectly matched layers?

We have an adaptive mesh refinement (AMR) code for solving the elastic wave equation with frictional fault interfaces (based on Chombo for those that are interested). One of the things that we have realized is that our results are being strongly…
Jeremy Kozdon
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4 answers

Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing Brownian dynamic motion (thermal motion) alternating…
NuclearAlchemist
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Solving the quadratic in the Fast Marching Method

The Fast Marching Method is a way of solving the Eikonal Equation on a discrete grid, essentially just computing a wavefront speading out from initial points, IE: The idea is that we want to compute the time at which a wavefront, moving across a…
Phylliida
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One-sided non-linear least squares with linear constraints

I am trying to solve a one-sided non-linear least-squares problem with linear constraints, i.e the problem: $\min_{\mathbf{x}} \quad \sum^m_{i=1} \mathbf{r}_i(\mathbf{x}) \qquad \text{ s.t } \quad A\mathbf{x} \leq…
OscarB
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Red(-Green)-Refinement vs. Newest-Vertex-Bisection

What are the "Pros and Cons" for these two methods of mesh-refinement? Both seem to be the prevalent methods. I can naturally imagine that global red refinement is comparatively easy to implement and attractive for research in multigrid-methods,…
shuhalo
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3 answers

plotting discontinuous functions

I need help plotting the Heaviside function: Real analysis often involves constructing bizarre functions which are intuitively correct, but ultimately wrong. See the great book Counterexamples in Analysis. I wrote a numpy script to plot the…
john mangual
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Publishing a software package along with a paper: licensing

I want to publish the software package I've written for my graduate work along with a paper describing the package. So far I've been considering liberal licenses such as BSD. However, I am now aware that publishing your code may involve an agreement…
AlexE
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5 answers

Good Finite Element Library for a small project

I'm currently working on this project and I have a basic structural analyzer that uses the finite element method. Essentially, I turn each block into a set of trusses, construct a stiffness matrix relating each truss's force to each other, and feed…
Chris Conlon
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