43 votes

Good examples of "two is easy, three is hard" in computational sciences

One example that appears in many areas of physics, and in particular classical mechanics and quantum physics, is the two-body problem. The two-body problem here means the task of calculating the ...
  • 2,792
36 votes

Good examples of "two is easy, three is hard" in computational sciences

In one and two dimensions, all roads lead to Rome, but not in three dimensions. Specifically, given a random walk (equally likely to move in any direction) on the integers in one or two dimensions, ...
30 votes

Good examples of "two is easy, three is hard" in computational sciences

A famous example is the boolean satisfiability problem (SAT). 2-SAT is not complicated to solve in polynomial time, but 3-SAT is NP-complete.
28 votes

Good examples of "two is easy, three is hard" in computational sciences

In social choice theory, designing an election scheme with two candidates is easy (majority rules), but designing an election scheme with three or more candidates necessarily involves making trade-...
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26 votes

Good examples of "two is easy, three is hard" in computational sciences

Here's one close to the hearts of the contributors at SciComp.SE: The Navier–Stokes existence and smoothness problem The three-dimensional version is of course a famous open problem and the subject ...
16 votes

Good examples of "two is easy, three is hard" in computational sciences

Simultaneous diagonalization of two matrices $A_1$ and $A_2$: $$ U_1^T A_1 V = \Sigma_1,\quad U_2^TA_2V=\Sigma_2 $$ is covered by existing generalized singular value decomposition. However, when the ...
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11 votes
Accepted

How important is learning hardware/architecture for scientific computing?

I haven't worked in quantum chemistry specifically, but I've worked in other areas where high performance is a correctness requirement (along with scientific accuracy), so I think we're on the same ...
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10 votes

Good examples of "two is easy, three is hard" in computational sciences

There are plenty of examples in quantum computing, although I've been out of this for a while and so don't remember many. One major one is that bipartite entanglement (entanglement between two ...
9 votes
Accepted

Computer Build for Scientific Computing

Many of us in scientific computing simply have well-equipped laptops for regular software development tasks, some multicore workstations for smaller-scale testing, and access to clusters for larger ...
7 votes

Good examples of "two is easy, three is hard" in computational sciences

Angle bisection with straightedge and compass is simple, angle trisection is in general impossible.
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7 votes

Good examples of "two is easy, three is hard" in computational sciences

Here's a neat one from optimization: the Alternating Direction Method of Multipliers (ADMM) algorithm. Given an uncoupled and convex objective function of two variables (the variables themselves ...
6 votes

Borrow computational power from machines around me

You could install BOINC on those machines. When the computers become idle, the BOINC screensaver/client requests tasks from a server and computes them. See more information about it here. This is ...
6 votes

What determines the usual chemistry textbook plots of atom orbitals?

Your intuition is right, for example in 3D Orbitals (German Wikipedia) the caption explicitly states that 90% iso-surfaces are used. I have however seen different percentages before where the results ...
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6 votes

Good examples of "two is easy, three is hard" in computational sciences

A smooth curve of degree 2 (i.e. given as the solution of $f(x,y) = 0$ where $f$ is a polynomial of degree 2) with a given point is rational, meaning that it can be parameterized by quotients of ...
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5 votes
Accepted

What equation should I fit this set of data points to?

You could either fit a logistic function (possibly composing it with a linear function), use segmented regression, or classification and regression trees, among other options. The original data, ...
5 votes
Accepted

Borrow computational power from machines around me

You can use HTCondor that is designed exactly to "steal" cpu cycles from remote machines. It may be a little difficult to setup but I think this may be the best approach.
5 votes

Global optimization methods in computational chemistry

You say you're mostly interested in geometry optimization. From a software point of view, here are a couple to get you started. USPEX, which works with crystals, isolated molecules and nanoparticles, ...
5 votes
Accepted

Maximize a function of an orthogonal matrix

There are specialized methods for the minimization of a differentiable function $f(X)$ subject to the orthogonality constraint $X^{T}X=I$. See for example: Lai, Rongjie, and Stanley Osher. “A ...
4 votes

How does one determine the point group of a molecule?

I'm happy to answer that there's a high-quality open source code for this: https://github.com/mcodev31/libmsym libmsym is a C library dealing with point group symmetry in molecules. It can ...
4 votes

Good examples of "two is easy, three is hard" in computational sciences

Type inference for Rank-n types. Type inference for Rank-2 is not especially difficult, but type inference for Rank-3 or above is undecidable.
4 votes

What are the things I should keep in mind before doing an analysis of my gromacs simulation?

I think that this question is too generic for a complete answer, as the latter would depend entirely on what you are simulating and what observables you are interested in. The only things that come to ...
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4 votes

Good examples of "two is easy, three is hard" in computational sciences

The problem on which I originally made that comment is a linear algebra problem: consider the linear matrix equation $$ \sum_{i=1}^k A_i X B_i = C, $$ where $A_i,B_i,C \in \mathbb{R}^{n\times n}$ are ...
4 votes
Accepted

Getting started with Computational Chemistry

Computational chemistry is a broad field, even more nowadays with increasing number of machine learning applications related to chemistry. As you have not specified what you are after I will suppose ...
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4 votes

Applications of Julia in Chemistry and Molecular Physics?

It's an entire programming language with a large community, so it's pretty much impossible to dig up all examples of its usage in these fields, but I can point to a few resources to get you started. ...
4 votes

How important is learning hardware/architecture for scientific computing?

I want to support the response from @Pseudonym, who makes the point that not everyone in the team needs to contribute to every aspect of the project. Something related to consider is that you are ...
4 votes
Accepted

Quasi-Newton Method with a Transformed Hessian

It might help us give a better answer if you give more details of your problem. But I think what's going on is effectively elimination of equality constraints. I'll take just translation as an example....
4 votes

Does it make any sense to acquire some sort of knowledge about manufacturing or engineering for computational design optimization?

Computation science lives by the grace of computing something. So if you learn about that something you will 1. make yourself more employable as an engineer, specializing in computational stuff, or 2. ...
3 votes

What equation should I fit this set of data points to?

An assortment of curves for fitting chemistry examples is presented in these Colby College class notes. Of particular application is the sigmoid response curve with variable "slope" for the central ...
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3 votes

Solve rate equations with different reaction orders using SciPy ode

First of all, there seems to be an inconsistency between the equation you wrote for $r_w$ and the code (a minus sign). Then, there are two issues with your problem: As indicated in the comments, ...
  • 6,091
3 votes
Accepted

Quantum Chemical Calculations is there a book for which method to use with what problem?

There is no universal answer to this. You will have to find publications that have similar set-ups and already did the benchmarking, or you will have to do it yourself. Once you understand how the ...

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