# All Questions

7,522 questions
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 ...
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 ...
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 ...
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 ...
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.
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 ...
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 ...
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,...
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?
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. ...
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 ...
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 ...
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 ...
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 ...
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 ...
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. ...
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 ?
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 ?
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 ?
6k views

### What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?