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1500 questions
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N-body simulation optimisation, looking for name or existing work

during the development of my N-body simulation with visualisation in WebGL, I devised an optimisation, and I'm wondering if it has a name. I find it unlikely that it has never been done before. It works like this: During the first timestep, make an…
Magnus Wolffelt
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Ways to start ab initio MD from classical MD

I am running molecular dynamics simulations of water for testing purposes. The box is quite small, if you ask a guy running classical MD, and relatively large, if you ask a DFT guy: I have 58 water molecules in periodic boundary conditions. To save…
Miguel
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Library with polylogarithm function

I am looking for a reliable library where I can find polylogarithm function and newton/secant method for solving non-linear equations. Basically I have something like this: f(x) = x - A*PolyLog(3/2, B*Exp(-t*x)) f(x) = 0 and f(x,y,z) = 0 g(x,y,z)…
Bociek
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Using global variables when doing scientific computing

I was taught in my freshman college computer programming course that using global variables is almost always a bad idea. However, I have found that when designing Fortran programs for very complex simulations, such a practice seems to make things…
Craig Feinstein
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Poisson equation finite-difference with pure Neumann boundary conditions

I'm trying to solve a 1D Poisson equation with pure Neumann boundary conditions. I've found many discussions of this problem, e.g. 1) Poisson equation with Neumann boundary conditions 2) Writing the Poisson equation finite-difference matrix with…
Charles
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Hardware performance, floating point functions

First of all, hope I've found the right forum for this question, if I haven't please pass me on to one which would fit better. Out of curiosity from an argument with someone who may or may not be more into CPUs than I am. We were arguing about the…
mathreadler
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Which numerical methods preserve time reversal symmetry?

If I have a physical system which contains a time reversal symmetry (for example a Hamiltonian $H(x,p)=p^2/2m + V(x)$ with $V(x)$ real) and I want to solve the differential equations which describe this system, which solver for ODEs should I use in…
Merlin1896
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Second order tensor field visualization software

Is there an overview available over tensor visualization software? My personal preference is: A software which is free, well documented, and offers visualization techniques for different physical second order (or higher-order) tensor fields. Some…
imranal
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Are there tasks in machine learning which require double precision floating points?

Double-precision calculations are significantly slower or more expensive than single-precision calculations. For example, the NVidia Tesla which performs well on doubles is much more expensive then regular GPU. At the same time I do not know about…
Marat Zakirov
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Meaning of search methods and optimization methods

I was wondering what differences and relations are between "search methods" and "optimization methods"? Especially when solving an optimization problem? I emphasize the context of solving optimization problems, because I guess search methods are…
Tim
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How to generate neighbors in hill climbing algorithm?

Hill climbing seems to be a very powerful tool for optimization. However, how to generate the "neighbors" of a solution always puzzles me. For example, I am optimizing a solution $(x_1, x_2, x_3)$. Here $x_1$ is in range $(0, 0.1)$, $x_2$ is in…
CuriousMind
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Iterative "solver" for $x^t \Sigma^{-1} x$

I can't imagine I'm the first to think about the following problem, so I'll be satisfied with a reference (but a complete, detailed answer is always appreciated): Say you have a symmetric positive definite $\Sigma \in \mathbb{R}^{n \times n}$. $n$…
Yair Daon
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Can MPI messages be prioritized?

As far as I understand, the order in which non-blocking point-to-point MPI messages (Isend and Irecv) are received is consistent with the order in which they are sent. Are there any techniques for giving certain messages priority over others? For…
Matthew Emmett
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Multigrid on "not perfectly rectangular" grid

Multigrid introductions normally use a rectangular grid. Interpolation of values is then straight forward: Just interpolate linearly on the edge between two adjacent nodes of the coarse grid to find the value of the fine grid node on that edge. For…
Michael
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Rank structure in the Schur complement

I am doing research on the structure in the Schur complements and find an interesting phenomenon: Suppose that A is from 5--pt laplacian. If I use nested dissection ordering and multifrontal method to compute the LU factorization and then check the…
Willowbrook
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