# All Questions

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### Pauli repulsion contribution in electronic structure computations

I am looking for a method to estimate the contribution from Pauli repulsion to the interaction energy of a molecular dimer in an electronic structure computation (e.g. with Density Functional Theory). ...
187 views

### Texture analysis methods modern survey paper

I want to study the methods of analyzing textured images. So i searched google scholor but only found very old papers statistical and structural approaches to texture 1979 haralick Image Texture ...
130 views

### Using an approximation algorithm to adapt parameter values of a given algorithm

Problem: I have an incremental online clustering algorithm which need 4 parameters that should be specified by the user before execution. The algorithm will gives "good results" if "a good parameter ...
187 views

### What mapping strategy should I use when solving many large linear systems of equations?

I am working on a problem that involves solving many (thousands) of distinct linear systems of equations, each with thousands of variables. Let's assume that the size of each matrix is exactly the ...
326 views

### How does one handle the source term in the Shallow Water Equations when using the discontinuous galerkin method? [closed]

I use the discontinuous galerkin method to solve the steady flow 1D shallow water equations with a bump at the bottom. This flow is frictionless. I use the runge-kutta method to approximate the time ...
1k views

### Diffusion kernel "guide"

Diffusion kernels are kernels which "project" information about graphs into $R^n$ so that certain machine learning techniques can be performed. I have read through this paper and feel fairly ...
178 views

### 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 ...
487 views

### Implementing a fair scheduling policy on Maui/Torque

We have Maui and Torque on our lab's UNIX cluster. Right now, all jobs are served by FIFO. We'd like to implement a more fair policy, but I have not successfully implemented it. The online ...
150 views

### 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 ...
202 views

### Power series approximation for any function such as $-e^{x^{2}}$ in some easily-accessed open-source software?

My comrades repeatedly encourages monotonous problems where the issue is the same: chain-rule and some basic arithmetic. Is there some computational way to derive power series approximations? Suppose ...
271 views

### 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 ...
934 views

### Can I use an explicit time stepping scheme to determine numerically whether an ODE is stiff?

I have an ODE: $u'=-1000u+sin(t)$ $u(0)=-\frac{1}{1000001}$ I know that this particular ODE is stiff, analytically. I also know that if we use an explicit (forward) time stepping method (...
2k views

### How useful is PETSc for Dense Matrices?

Wherever I have seen, PETSc tutorial/documents etc. say that it is useful for linear algebra and usually specifies that sparse systems will benefit. What about dense matrices? I am concerned about ...
336 views

### Working with multi-dimensional functions

How would you represent functions of type $[-1, 1]^n \to \mathbb R \;$ for moderate $n$? How would you integrate them? For small $n$ (1-2) such functions can be represented as histograms, vectors in ...
385 views

### Databases of results for numerical codes

In the numerical methods literature, many research papers consist of a description of a new algorithmic variation, followed by a few test problems comparing the new method with one or two existing ...
1k 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 ...
1k views

170 views

### How to print out a network in peersim? [closed]

Peersim is a peer-to-peer network simulator. I'm simply trying to get the program to print out the network (an edge list is fine). Presumably this is possible, since there is an in-built ...
126 views

### Low performance on sge cluster

I'm having an issue with my project. When I run the code of Monte-Carlo simulation, on the local server (the machine in my office) it runs on a rate of roughly 100000 steps per 24 hours. When I run it ...
2k views

### Schrodinger equation with periodic boundary conditions

I have a couple of questions regarding the following: I am trying to solve the Schrodinger equation in 1D using the crank nicolson discretization followed by inverting the resulting tridiagonal ...

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