Avogadro2



For reason that I did not understand Avogadro has been phased out of Ubuntu 20.x and the available package Avogadro2 is instead another branch of the package, which unfortunately does not cover all the features. As it appears impossible to install that older but more powerful version of Avogadro on last Ubuntu, does anyone know if it is still possible to delete selected atoms? Amedeo Avogadro, Italian mathematical physicist who showed in what became known as Avogadro’s law that, under controlled conditions of temperature and pressure, equal volumes of gases contain an equal number of molecules. Learn more about Avogadro’s life and career. Stl mugshots 63104 Avogadro version avogadro2-libs-1.90.0-12 Qt: 5.9.2 Desktop version OS: Linux Scienfitic Linux (compatible with Redhat EL7) Version: 7.6 Compiler: gcc-c+±4.8.5-39.el7.x8664, cmake-2.8.12.2-2.el7.x8664 Describe the bug I am making a package of “avogadro2-libs-1.93.0-1.fc32” on the RHEL7 platform. But, the build fails in.

  1. Avogadro 2 Download
  2. Avogadro's Number
  3. Avogadro
  4. Avogadro's Law Calculator
  5. Avogadro Bo2

Dear All,

Avogadro 2 is a chemical editor and visualization application, it is also a set of reusable software libraries written in C using principles of modularity for maximum reuse. The development of the first generation Avogadro application and library is documented in our paper, and this remains the preferred method of citation at present. The motivation for rewriting Avogadro, along with. You can download the latest binaries here, or access the current development version using Git.

Currently, I make use of avogadro2 on my desktop which is running Ubuntu 20.04. The binaries are from the deb packages supplied by avogadro and libavogadro2-1.

I have noticed that the “Quantum–>Input generators” pull down is absent. I have also noticed that the “plugin downloader” does not work either, but I think this a separate issue (I think it’s putting them in the wrong location).

Avogadro 2 Download

Anyway, I manually moved the scripts to the expected location:
~/.local/share/OpenChemistry/Avogadro/inputGenerators
but this did not work. I also note that a few people may also be experiencing this too:

Anything that’s not a script will get ignored. On launch, it will go through the files and track which ones it can run. We decided not to restrict extensions because someone might want to write in Shell or Ruby or Julia or whatever. The point of downloading is that you can update those scripts without needing a new release of Avogadro. The versions you downloaded are likely slightly newer than in the last released version. I don’t remember offhand if there’s something new, but I think PySCF wa…
Avogadro2
For the Mac, should that directory exist already with the binary install of Avogadro2? I checked Library/Application Support for both the system and my user account and neither had an OpenChemistry folder. Manually creating the folders and placing the various .py files there didn’t seem to help Avogadro2 to find them.

So, to investigate, I compiled avogadro2 from source, from the git repo:

This worked; I was able see “Quantum–>Input generators” and all the input generators. So… my attention turned to the compilation and packaging that Ubuntu was using.

Next, I compiled the src debian packages (https://launchpad.net/ubuntu/+source/avogadrolibs/1.93.0-3 and https://launchpad.net/ubuntu/+source/avogadro/1.93.0-1) and installed the generated debs. I, again, saw the original problem.

Now, I suspect there is a bug with the packaging process (the actual compile processes are in ./debian/rules in this file ).

I also notice that from the terminal, the deb binary does not report looking for the input generator (see 'Checking for “foo” … '):

But, the version compiled from the git source, does:

My current theory is the absence of avogadrogenerators in the deb package building process could be the issue and somehow prevents the final binary from searching fro input generators. This is just speculation at the moment…

I am still working my way through the related code, but I just wanted to document what I had found thus far.

What do you think?

Thanks,

Mark


GSoC is coming to a close! It has been a productive summer working with Avogadro2. I was able to complete all of my primary goals and contribute in a few extra areas as well.
Work Accomplished
Here is a list of the major contributions that I was able to make towards the project:

Avogadro's Number

  • Added POSCAR (from Vienna Ab Initio Simulation Package) format reader and writer. This is used by a lot of computational materials science groups.
  • Added an 'Import Crystal from Clipboard' feature. This was present in Avogadro 1 and allows the user to copy a crystal file to their clipboard and import it from there. It is particularly useful for POSCAR format due to the way files are named.
  • Added a supercell builder. This is helpful for visualization and situations that require a supercell.
  • Added spglib to Avogadro2. Spglib is a library written in C that allows for many useful crystal operations related to symmetry and space groups.
  • Added space group perception using spglib.
  • Added functions using spglib that allow users to primitive reduce a crystal, conventionalize a crystal, and symmetrize a crystal.
  • 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.
All of these features are accessible by the user interface so that users may access them as well. In addition, tests were made for the majority of these features to demonstrate that they work.
Avogadro

Here is a list of minor contributions (that were not in my primary goals) that I was able to make towards the project:
  • Added undo/redo operations for already existing crystal features and newly added crystal features.
  • Added undo/redo text in the user interface to clarify the operation that would be performed.
  • Improved the cmake files so that VTK can be more easily turned on or off.

Avogadro


  • Fixed a few bugs in crystal functions (one involving transforming atoms and one involving setting the cell parameters).
  • Improved cmake files so that some options were set at the right time.
  • Fixed GUI bug where the center and radius of a scene were not being updated properly (this resulted in clipping).
  • Fixed a few small memory leaks in an assignment operator.
  • Fixed some bugs in the atomic coordinate editor (and improved it so that the user experience is smoother).

Avogadro2
Descriptions and further discussion of the major contributions can be found at the following two links:
Contributions before midterm (June 27):
Contributions after midterm (June 27):
A more detailed look at the code changes that were made can be viewed from the following links. The commits that were a part of the GSoC work are from about May 10, 2016 to August 23, 2016. Links are ordered by decreasing number of commits:
In addition, for Avogadro 1, I was able to assist in creating the new Windows executable for the new release: Avogadro 1.2.
Work Still in Progress
Although I finished my primary goals for Avogadro 2, I started some extra work that I will continue working on after GSoC ends. Probably the most significant is adding YAeHMOP (Yet Another extended Hückel Molecular Orbital Package). This can allow Avogadro to perform quick semi-empirical quantum mechanical calculations using Extended Hückel Theory. I mentioned this in more detail on my blog post containing my contributions after the midterm, but this feature could potentially add many different types of quick semi-empirical quantum mechanical calculations that could be useful when analyzing a molecule or crystal. I've been adding it to Avogadro 1 first, and then I'll be adding it to Avogadro 2 next. My work so far with preparing YAeHMOP for Avogadro can be found here:
https://github.com/greglandrum/yaehmop/commits?author=psavery
I've also been working on improving the undo/redo operations while drawing to make it more user-friendly, and I've been adding more undo/redo operations to different features.

Avogadro's Law Calculator

In conclusion, my work this Summer seems to have been fairly successful! I'm glad that Avogadro2 has these new additions, and I hope it does well in the future!

Avogadro Bo2

Thanks for reading!