Aggregator

Atomic Modeling with GAMGI

2 months ago
by Joey Bernard

For this article, I'm moving back into the realm of chemistry software—specifically, the General Atomistic Modelling Graphic Interface, or GAMGI. GAMGI provides a very complete set of tools that allows you to design and visualize fairly complex molecules.

GAMGI has the special ability to make creating repeating structures much easier, which is handy when you're trying to create crystalline structures.

GAMGI should be available in the package repositories of most Linux distributions. For example, on Debian-based distros, you can install GAMGI with the following command:

sudo apt-get install gamgi

There are also data and documentation packages (gamgi-data and gamgi-doc), and when you first start to use GAMGI, it's a good idea to install those packages as well.

Once the packages are installed, you can start GAMGI from the command line or from your desktop environment's menu system. When it starts up, you get a blank canvas to begin your work.

Figure 1. When you start GAMGI, you get a minimal set of tools to help begin your project.

This interface is probably one of the more minimal ones of the chemistry packages that you are likely to use, but it hides all of the functionality that is present within GAMGI. It is object-oriented, in that all of the main elements are treated as independent objects, with properties and relationships to other objects. These elements include atoms, bonds, molecules and crystal planes. Each of them are built up of a number of the earlier ones. One extra piece that GAMGI has is the ability to work with orbitals. Let's walk through an example of a salt crystal (NaCl) to show how you can use GAMGI to do graphical analysis.

When looking at a crystalline structure, you'll want to start by creating a cell in the window. You do this by clicking the Cell→Create menu item. Then you'll get a pop-up window where you can set several properties of the new cell.

Figure 2. When you create a new cell for crystal structures, you can set several different properties on how it will be constructed.

Since salt is a cubic crystal, you'll want to set the system value to c (for cubic), and set the lattice value to F (for face-centered). For each of these, you can get a full set of allowed values by clicking the associated "List" button. Clicking Ok creates the cell.

Go to Full Article
Joey Bernard

System76's New Manufacturing Facility, Ubuntu 17.10 Reaches End of Life, Google Cloud Platform Marketplace, Stranded Deep Now Available for Linux and Cutelyst New Release

2 months ago

News briefs for July 19, 2018.

System76 has moved into its new manufacturing facility in Denver, Colorado. The company will begin making computers in the US, rather than just assembling them. See the System76 blog post for photos of the new digs.

Ubuntu 17.10 "Artful Aardvark" has reached end of life today, so there will be no more security updates for that version. If you're running Ubuntu 17.10, you need to upgrade to 18.04 now. See the post on It's FOSS for more information and instructions on how to upgrade.

Google has rebranded its Cloud Launcher platform, and it now will be called the Google Cloud Platform Marketplace (or GCP Marketplace). LinuxInsider reports that "it will offer production-ready commercial Kubernetes apps, promising simplified deployment, billing and third-party licensing."

Single-player survival game Stranded Deep is now available for Linux, GamingOnLinux reports, although users were reporting a few issues earlier this week. Stranded Deep is available on Steam.

Cutelyst, a C++ web framework based on Qt, has a new release. The update includes several bug fixes and some build issues with buildroot. See Dantti's Blog for all the details. Cutelyst is available on GitHub.

News System76 Ubuntu Google Kubernetes gaming qt
Jill Franklin

Using the Best CPU Available on Asymmetric Systems

2 months ago
by Zack Brown

Dietmar Eggemann posted a patch from Quentin Perret to take advantage of energy-efficient CPUs on asymmetric multiprocessor (AMP) systems. AMP is distinguished from SMP (symmetric multiprocessor) systems in that an SMP system uses several instances of only one type of CPU, while an AMP system might use CPUs of differing speeds, feature-sets and so on.

Quentin's patch was an effort to take advantage of differences in power consumption between the CPUs on an AMP system. It attempted to identify the most efficient CPU that was not already saturated with processes and assign newly awakened processes to it. If no CPUs fit the bill, standard SMP-type methods of processor assignment would be used instead.

Dietmar explained, "The selection of the most energy-efficient CPU for a task is achieved by estimating the impact on system-level active energy resulting from the placement of the task on each candidate CPU. The best CPU energy-wise is then selected if it saves a large enough amount of energy with respect to prev_cpu."

He acknowledged that this algorithm was a brute-force approach that could work well only on systems with a relatively small number of CPUs. He said, "This patch is an attempt to do something useful, as writing a fast heuristic that performs reasonably well on a broad spectrum of architectures isn't an easy task."

Patrick Bellasi and Joel Fernandes had no serious objections to the patch and offered some technical suggestions. The discussion delved into various technical issues and specific ways of addressing them, with no one raising any controversial issues.

This is the type of situation with a patch where it might look like a lack of opposition could let it sail into the kernel tree, but really, it just hasn't been thoroughly examined by Linux bigwigs yet. Once the various contributors have gotten the patch as good as they can get it without deeper feedback, they'll probably send it up the ladder for inclusion in the main source tree. At that point, the security folks will jump all over it, looking for ways that a malicious user might force processes all onto only one particular CPU (essentially mounting a denial-of-service attack) or some such thing. Even if the patch survives that scrutiny, one of the other big-time kernel people, or even Linus Torvalds, could reject the patch on the grounds that it should represent a solution for large-scale systems as well as small.

Go to Full Article
Zack Brown