One of them involves undo and redo commands. The difference, however, is that the positions of the atoms have also been idealized so that they should be in nearly perfect positions for the space group.Īs I mentioned at the top of the blog, I've been able to do work on some additional things with Avogadro2 as well. So this is similar to a "Reduce to Primitive" feature in that way. Notice that the number of atoms has been reduced, and the unit cell is a lot smaller. The result of symmetrizing the filled unit cell of post-perovskite is the following: So "Symmetrize" idealizes atom positions and reduces the crystal to its smallest form. "Reduce to Primitive" does not do either of these things, but it reduces the crystal to the smallest form in which it can be represented. "Conventionalize Cell" idealizes the atom positions to match those of the space group, and it changes the unit cell to be in its conventional form (as defined by its Bravais lattice). It's probably best to think of "Symmetrize" as a combination of "Conventionalize Cell" followed by "Reduce to Primitive," although it does it in one operation to save time and memory. The result for post-perovskite is the following: Once a space group has been chosen, the fill unit cell feature will apply the symmetry operations to every atom in the crystal. The Select Space Group dialog is a scroll-able table containing all of the space groups - it looks like the following: This is necessary because the space group cannot be determined from an asymmetric unit since it does not yet have the correct symmetry. Once "Fill Unit Cell" is selected from the dropdown menu, it will ask the user to select a space group. In Avogadro2, you now just need to select it from the dropdown menu as shown in Figure 2:įigure 2: Fill Unit Cell in Dropdown Menu This is done with the "Fill Unit Cell" feature. You find the other atoms by applying symmetry operations for the space group to the existing atoms. The cell looks rather empty, doesn't it? That's because only the necessary atoms are included. Magnesium is green, silicon is grey, and oxygen is red. In Avogadro2, this looks like the following:įigure 1: Asymmetric Unit of Post-Perovskite (MgSiO3) For post-perovskite, that may look something like this (data from here ): It's common for papers in journals and databases to give a crystal's information as its asymmetric unit. Don't worry about those details too much, though, if you aren't familiar with them. This means the Bravais lattice is of type C, and it has two mirror planes (the m's) and a glide plane (the c). It is stable under the pressures there, and it has important properties as far as geophysics is concerned. This material is reportedly common in the mantle of the earth. This will be explained more as we go along.įor an example, let's take post-perovskite (MgSiO3). I'll be discussing a few of the new ones that I have added here.įirst of all, I've added two features called "fill unit cell" and "reduce to asymmetric unit." These two features can be thought of as opposites of one another. I've mostly been adding operations related to crystal space groups for the molecular editor. My blog post after the midterm evaluations was here: Google Summer of Code 2016 is coming to a close! Fortunately, I've been able to accomplish my primary goals for Avogadro2 and a little more. In addition, tests were made for the majority of these features to demonstrate that they work. Added functions to fill a unit cell by using symmetry operations for a space group, and added functions to reduce a unit cell to its asymmetric unit.Īll of these features are accessible by the user interface so that users may access them as well.Added functions using spglib that allow users to primitive reduce a crystal, conventionalize a crystal, and symmetrize a crystal.Added space group perception using spglib.Spglib is a library written in C that allows for many useful crystal operations related to symmetry and space groups. This is helpful for visualization and situations that require a supercell. It is particularly useful for POSCAR format due to the way files are named. This was present in Avogadro 1 and allows the user to copy a crystal file to their clipboard and import it from there. Added an "Import Crystal from Clipboard" feature.This is used by a lot of computational materials science groups. Added POSCAR (from Vienna Ab Initio Simulation Package) format reader and writer.
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