Computational Science Stack Exchange
Computational Science Stack Exchange

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1500 questions
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5 answers

External hardware resources for running long and computationally intensive simulations

I've written code for an obstructed random walker simulation and I want to run long simulations (6 hours or more on my computer). I don't want to run this simulation on my computer because I will want to run multiple simulations simultaneously and I…
Ami
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2 answers

Understanding OpenCL performance

I'm using ViennaCL's interface to Eigen as a way to leverage OpenCL. Specifically, I'm using the ::viennacl::linalg::bicgstab_tag with an Eigen sparse matrix. However, the performance isn't what I hoped that it would be. What tools on Windows…
Joseph Winston
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Do C++ matrix libraries translate compound vector operations to single loops?

I am trying to replicate Fortran90 array syntax using a C++ library. The libraries themselves are discussed at length in this question. They can all do something like this: D = alpha*A + beta*B + gamma*C for vectors A, B, C and scalars alpha,…
Max Hutchinson
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3 answers

C - OpenMP, MPI, Serial Program

I'm part of a Computational Science course and come from a non-programming background, so please forgive me my ignorance. I'm working on a set of code in C to numerically solve the Navier Stokes equations for a Computational Fluid Dynamics course.…
kfkhalili
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Poisson equation with Neumann boundary conditions

I'm trying to solve the Poisson equation with pure Neumann boundary conditions, $$ \nabla^2\phi = \rho \quad in \quad \Omega\\ \mathbf{\nabla}\phi \cdot \mathbf{n} = 0 \quad on \quad \partial \Omega $$ using a Fourier transform method I found in…
Grieverheart
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7
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4 answers

biharmonic equation

I want to solve the biharmonic equation numerically, that is: $$\Delta^2 u=f~~in~~\Omega$$ $$u=g_1~~on ~~\partial \Omega$$ $$\frac {\partial u}{\partial n}=g_2~~on ~~\partial \Omega$$ Using Green's formula, we have that if $u$ is smooth enough …
rosa
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7
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3 answers

FOSS tools for creating high quality physics animations and simulations in 2d and 3d

If I want to create a high quality figure to illustrate a scientific concept or experiment I usually use tikz together with pgfplots or pstricks. However this is for static content. Both tools are extremely powerfull for it's purpose and give high…
Julia
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1 answer

Sparse hermitian eigensystems: are there better techniques than Arpack or TRLan?

As a part of other work I need to solve relatively large (~1E5x1E5) and sparse (~100 non-zero elements in each raw in few blocks) hermitian eigensystems. Usually only few eigenvalues+vectors are needed, but with high precision. Currently I am using…
Misha
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2 answers

Open-access journals in Computational Science

In light of the recent petition to boycott Elsevier, I was wondering what options we have in Computational Science for Journals which are completely open-access, Journals which allow/support open-access articles. I am aware that there are quite a…
Pedro
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Conjugate Gradient with Hierarchical Basis Functions: How can the hierarchical base be decomposed?

I'm trying to implement a Conjugate Gradient solver using Hierarchical Basis Functions, following this paper. In section 3 the paper says that the hierarchical basis matrix $S$ can be decomposed into a "series of very sparse matrices $S =…
rsp1984
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7
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1 answer

High quality flexible GMRES (FGMRES) implementation

What are the best FGMRES implementations in various languages/frameworks? In particular, are there any good quality Matlab implementations? I am referring to the variation of GMRES where a changing or nonlinear preconditioner is allowed by keeping…
Nick Alger
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1 answer

Type of Navier-Stokes equation

What type equation Navier-Stokes is: Elliptic, parabolic, or hyperbolic? Should it give always the same answer no matter what is the initial condition? How these statements could be proved?
Shibli
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7
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2 answers

Can quantum methods be applied to the protein-ligand docking problem?

In the problem of protein-ligand docking, most of the time people are happy if they can just predict the final conformation the ligand adopts into the protein's binding pocket. Most of the time one can just use a physical based scoring function and…
Open the way
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2 answers

Least Squares and Fourier Series

I have a little bit of problem figuring out the relation between Fourier series and Least Squares. As far as I understand, LS is a way of minimizing the quadratic error between a measured value $y_i$ and a linear combination of functions evaluated…
BRabbit27
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2nd order centered finite-difference approximation of $u_{xy}$

The problem is to find a 2nd order finite difference approximation of the partial derivative uxy, where u is a function of x and y. Page 5 of this pdf I found does a centered difference approximation it in two steps. It first does the 2nd order…
Abhranil Das
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