# Questions tagged [efficiency]

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### What is the computational cost of $\sqrt{x}$ in standard libraries?

One of the major issues that we have to deal with in molecular simulations is the calculation of distance-dependent forces. If we can restrict the force and distance functions to have even powers of ...
7k views

### What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?

I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY. Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
2k views

### I/O Strategies for computational problems with large data sets?

My research group focuses on molecular dynamics, which obviously can generate gigabytes of data as part of a single trajectory which must then be analyzed. Several of the problems we're concerned ...
870 views

### When is automatic differentiation cheap?

Automatic differentiation allows us to numerically evaluate the derivative of a program on a particular input. There is a theorem that this computation can done at a cost less than five times the cost ...
2k views

### What is the most efficient way to write 'for' loops in Matlab?

I have read that if, for example, I have a double for loop that runs over the indexes of a matrix, then putting the column running index in the outer loop is more ...
432 views

### Costs of lookups versus calculations

I am interested in setting up calculations to check if a distance criterion is satisfied: that is, the distance between a vector ${\bf x}_i$ and anther vector ${\bf x}_j$ should be less than some ...
842 views

### Is there a complexity between $O(n)$ and $O(n \log n)$ [closed]

Is there a complexity degree that is bigger than $O(n)$ and smaller than $O(n \log n)$?
3k views

179 views

### Performance based on the Roofline model

To somewhat follow up on the question asked here, I have been told that the Roofline model is one way of assessing the performance of any scientific code. Basically I compute the Arithmetic Intensity (...
72 views

### What is the fomula of polynomial time of solving positive definite symmetric linear system

For a positive definite symmetric linear system, Cholesky decomposition based method should be the best solver which has a rough n^3/3 flops requirement. What is ...
745 views

### Modern Computer Efficiency vs Modern Nervous Systems

I am currently working on an evolutionary system and most of what I have heard is that a computer like mine at the moment would be able to simulate a bee sized brain (not taking into account the time ...
180 views

### Difference between Brent's and Alefeld-Potra-Shi for root finding

I need to find the (unique) root of a nonlinear function $f(x)$, $x \in \mathbb{R}$. For the record, $f(x)$ is the CDF of a probability density minus a constant $0 < p < 1$ (I am inverting the ...
686 views

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### Stiff ODEs coupled with PDEs (computational efficiency)

I am simulating in COMSOL a system of 3 coupled PDEs (parabolic & elliptic) along with 10 stiff ODEs. In order to have the system working, I am downsizing the time step size too much to achieve ...
68 views

### Calculate proportions of exponentially weighted factors avoiding underflow problem

I am trying to implement in Python this ratio: $\frac{w_t(i)}{\sum w_t(j)}$ where $w_t(i) = w_{t-1}(i)\cdot\exp{(-x_{t}(i))}$, i.e. the weights are exponentially decreasing without running into ...
71 views

### What's the most efficient way to calculate the Wiger quasiprobability distribution?

I want to calculate the Wigner quasiprobability distribution function of a particular wavefunction. The definition suggests a few straightforward ways of calculating it, but I was wondering if there's ...
I have two variations of an iterative algorithm. All the steps of both algorithms are equivalent except one. In this step: Algorithm 1 needs to compute the matrix $ABA^T$ for matrices \$A \in \mathbb{...