All Questions

7
votes
3answers
434 views

Does there exist an arbitrary-precision convex optimization solver?

I have a relatively simple convex optimization problem that involves less than 100 variables but contains a terribly ill-conditioned matrix. I have tried CVX and CPLEX; even though both can typically ...
15
votes
1answer
1k views

When should implicit methods be used in the integration of hyperbolic PDEs?

Numerical methods for solving PDEs (or ODEs) fall into two broad categories: explicit and implicit methods. Implicit methods allow larger stable timesteps but require more work per step. For ...
22
votes
4answers
1k views

When is a high order method useful for computational fluid dynamics simulations?

Many numerical approaches to CFD can be extended to arbitrarily high order (for instance, discontinuous Galerkin methods, WENO methods, spectral differencing, etc.). How should I choose an ...
16
votes
2answers
756 views

How can I choose a good Riemann solver when numerically solving a system of hyperbolic PDEs?

Many numerical methods for hyperbolic PDEs are based on the use of Riemann solvers. Such solvers are essential for accurately capturing shock waves. There are a range of such solvers available for ...
15
votes
1answer
3k views

How can I estimate the condition number of a large sparse matrix using PETSc?

I have a PETSc Mat and would like to estimate its condition number.
10
votes
1answer
161 views

Polynomials that are orthogonal over curves in the complex plane

Various important sets of polynomials (Legendre, Chebyshev, etc.) are orthogonal over some real interval with some weighting. Are there known families of polynomials that are orthogonal over other ...
21
votes
1answer
10k views

Why is Newton's method not converging?

I am using PETSc's nonlinear solver package SNES to solve a system of nonlinear equations obtained by discretizing a partial differential equation. How can I determine why the solver is not converging ...
18
votes
2answers
287 views

Is there an efficient algorithm for matrix-valued continued fractions?

Suppose I have a matrix equation recursively defined as A[n] = inverse([1 - b[n]A[n+1]]) * a[n] Then the equation for A[1] looks similar to a continued fraction,...
5
votes
1answer
93 views

What are some good ICA packages for physiological data, like MEG?

EEGLab doesn't work well due to the data being from a Neuromag MEG. Any thoughts for alternatives?
16
votes
3answers
255 views

Uses of power series maps

I'm from the field of accelerator physics, specifically related to circular storage rings for synchrotron light sources. High energy electrons circulate around the ring, guided by magnetic fields. ...
7
votes
1answer
995 views

Alternative to Bron-Kerbosch algorithm for enumerating maximal cliques in inverse interval graphs

I often use inverse interval graphs to represent biologically relevant features along a genomic sequence. For example, given a (relatively) small genomic region, the graph would contain a node for ...
15
votes
3answers
5k views

How is B3LYP implemented in Gaussin 0*, GAMESS-US, Molpro, … etc?

Specifically I want to extend work involving B3LYP started with Gaussian 03 but continued with GAMESS-US. The energies provided by the default B3LYP methods are not the same. There is a discussion ...
7
votes
1answer
481 views

How can I tell VASP 5.2 is compiled with FFTW3?

When VASP 5 was released, the performance was mostly slower than our make of VASP 4.6. I wrote it off as an optimization issue, and went on in my life. Then, in VASP 5.2, with the release notes, I ...
14
votes
1answer
571 views

Complexity of MD simulations

I'm new to molecular dynamics (MD) simulations. What is the complexity of a molecular dynamics simulation in terms of simulation time? In other words, if I want increase the simulated time from 10 ...
17
votes
8answers
2k views

Parsing protein structure data in C

My background is in genomics, but I have recently been working with problems related to protein structure. I wrote a few relevant programs in C, building my own PDB file parser from scratch in the ...
17
votes
3answers
306 views

Desktop software with HPC resources for back end number crunching

Our workgroup produces a desktop application that simulates building energy performance. It is a .NET application and when the user is running a lot of simulations, they can be quite time consuming. ...
2
votes
3answers
3k views

Differences between Gaussian and Slater functions on the quality of the results?

Given two computational programs, one using a Gaussian basis, and the other using Slater basis, what are the practical differences, advantages and disadvantages for each choice ?
9
votes
2answers
499 views

What does it mean for a basis set to be “correlation consistent” ?

Some basis sets are said to be "correlation consistent". What does it mean in practice ?
7
votes
2answers
1k views

How to choose a basis set for ab-initio evaluations ?

How do I pick a basis set for an ab-initio Hartree-Fock evaluation ? In other words, what are the important characteristics of a basis set so that a proper choice can be made ?
13
votes
2answers
6k views

What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?
13
votes
3answers
366 views

Is Hartree-Fock always a good approximation for molecular geometries and no bond breaking ?

Are there cases where Hartree-Fock is not a good approximation to compute equilibrium geometry when the molecule is in a non bond-breaking condition?
7
votes
2answers
241 views

What is the difference between Coupled Cluster SD and SD(T)?

Can you explain the difference between these two computational methods ?

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