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It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18.04, and did a upgrade, it is replaced with Avogadro 2.

The original Avogadro had a very useful feature, where we could generate input files for several Quantum Chemistry packages. Now the problem is, Avogadro 2 doesn't seem to have the input generators as part of the base install, working out-of-the-box. It seems this functionality was moved to a set of plugins. I tried to get them working, by two different routes, but had no sucess so far. I'm describing what I tried to do, if somebody knows how to sort this problem.

First try: Built-in plugin downloader.

Opening Extensions > Plugin Downloader, we are presented the following screen:

enter image description here

By the description, avogenerators is what I'm looking for. When I select it, and click on Download Selected, it tells me the download was sucessful:

enter image description here

But when I go back to the work area, the menus are unchanged, even after reset. So I think this route failed.

Second try: Download with GIT

I seeked some guidance on this issue in the plugin page on github, but found only this remark:

Installing

These scripts need to be installed in a location where the Avogadro 2 application can find them. They use the JSON API described in the Avogadro 2 API documentation, but the best way to learn is to look at the existing scripts and adapt them to your needs.

Anyway, I proceeded to install GIT:

user@machine:~/src$ sudo apt install git-all

And try to clone the plugin repository:

user@machine:~/src$ git clone https://github.com/OpenChemistry/avogenerators.git
Cloning into 'avogenerators'...
remote: Enumerating objects: 211, done.
remote: Total 211 (delta 0), reused 0 (delta 0), pack-reused 211
Receiving objects: 100% (211/211), 70.05 KiB | 481.00 KiB/s, done.
Resolving deltas: 100% (130/130), done.

From this point it was not clear what to do. I tried to navigate from the Open button into the cloned project folder, and it recognizes the plugin.json file as something that can be opened:

enter image description here

But when you try to load the plugin, it just throws a error:

enter image description here

Third try (Update September 10, 2020): Git download in proper location.

Following the advice in answer comments, I tried to repeat the Git download of the plugins, but this time under ~/.local/share/OpenChemistry/Avogadro/inputGenerators, creating missing subfolders to complete the path, when needed:

user@machine:~$ cd ~/.local/share/OpenChemistry/Avogadro/
user@machine:~/.local/share/OpenChemistry/Avogadro$ ls
other
user@machine:~/.local/share/OpenChemistry/Avogadro$ mkdir inputGenerators
user@machine:~/.local/share/OpenChemistry/Avogadro$ cd inputGenerators/
user@machine:~/.local/share/OpenChemistry/Avogadro/inputGenerators$ git clone https://github.com/OpenChemistry/avogenerators.git
Cloning into 'avogenerators'...
remote: Enumerating objects: 211, done.
remote: Total 211 (delta 0), reused 0 (delta 0), pack-reused 211
Receiving objects: 100% (211/211), 70.05 KiB | 268.00 KiB/s, done.
Resolving deltas: 100% (130/130), done.
user@machine:~/.local/share/OpenChemistry/Avogadro/inputGenerators$ ls
avogenerators
user@machine:~/.local/share/OpenChemistry/Avogadro/inputGenerators$ cd avogenerators/
user@machine:~/.local/share/OpenChemistry/Avogadro/inputGenerators/avogenerators$ ls
dalton.py         inputgeneratortest.py  nwchem.py    pyscf.py
gamessuk.py       LICENSE                orca.py      qchem.py
gaussian.py       molpro.py              plugin.json  README.md
generators.cmake  mopac.py               psi4.py      terachem.py

Still didn't suceed.

Closing remarks

If I didn't just fumbled somewhere, and other people are able to reproduce the problem, I think this is a breaking issue, as the input generators should be critical to many people besides me. It would be nice if the original Avogadro were available in the repositories as a fallback in situations like this. All the tests in this posts were done in a machine running Mint 20 (Ulyana).

Edit

Given Geoff's answer telling the problem is probably related to the locations the plugins are expected to be, I did a search for the Avogadro related locations in my machine, as I think it may be useful.

user@machine:~$ sudo find / -iwholename *avogadro*
/home/user/.local/share/OpenChemistry/Avogadro
/home/user/.local/share/OpenChemistry/Avogadro/other
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/gaussian.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/LICENSE
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/gamessuk.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/inputgeneratortest.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/orca.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/psi4.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/generators.cmake
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/plugin.json
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/terachem.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/mopac.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/molpro.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/pyscf.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/nwchem.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/.github
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/.github/config.yml
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/.github/PULL_REQUEST_TEMPLATE
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/README.md
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/qchem.py
/home/user/.local/share/OpenChemistry/Avogadro/other/OpenChemistry-avogenerators-8444312/dalton.py
/home/user/.config/OpenChemistry/Avogadro.conf
/usr/lib/python3/dist-packages/avogadro
/usr/lib/python3/dist-packages/avogadro/__pycache__
/usr/lib/python3/dist-packages/avogadro/__pycache__/__init__.cpython-38.pyc
/usr/lib/python3/dist-packages/avogadro/__init__.py
/usr/lib/python3/dist-packages/avogadro/io.cpython-38-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/avogadro/core.cpython-38-x86_64-linux-gnu.so
/usr/lib/x86_64-linux-gnu/libAvogadroCore.so.1.93.0
/usr/lib/x86_64-linux-gnu/avogadro2
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/VanDerWaals.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/POVRay.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/CoordinateEditor.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Hydrogens.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Spectra.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/BallStick.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/commands.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Selection.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/NetworkDatabases.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Bonding.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Surfaces.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/ThreeDMol.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/MolecularProperties.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Manipulator.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Crystal.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/CrystalScene.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/LammpsInput.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/LineFormatInput.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Editor.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/SpaceGroup.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Wireframe.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/OverlayAxes.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/VanDerWaalsAO.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Meshes.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/BondCentric.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/OpenBabel.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/CopyPaste.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/CustomElements.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Force.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/MongoChem.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/MeasureTool.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Licorice.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/PlayerTool.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/ImportPQR.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/PluginDownloader.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/VRML.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Navigator.a
/usr/lib/x86_64-linux-gnu/avogadro2/staticplugins/Select.a
/usr/lib/x86_64-linux-gnu/avogadro2/scripts
/usr/lib/x86_64-linux-gnu/avogadro2/scripts/commands
/usr/lib/x86_64-linux-gnu/avogadro2/scripts/commands/scale.py
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/usr/lib/x86_64-linux-gnu/libAvogadroQtGui.so.1
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/usr/lib/x86_64-linux-gnu/libAvogadroRendering.so.1.93.0
/usr/lib/x86_64-linux-gnu/libAvogadroIO.so.1
/usr/lib/x86_64-linux-gnu/libAvogadroCore.so.1
/usr/lib/x86_64-linux-gnu/libAvogadroQtOpenGL.so.1.93.0
/usr/lib/x86_64-linux-gnu/libAvogadroQtOpenGL.so.1
/usr/lib/x86_64-linux-gnu/libAvogadroRendering.so.1
/usr/lib/x86_64-linux-gnu/libAvogadroIO.so.1.93.0
/usr/lib/x86_64-linux-gnu/libAvogadroQtGui.so.1.93.0
/usr/lib/x86_64-linux-gnu/libAvogadroQuantumIO.so.1.93.0
/usr/lib/x86_64-linux-gnu/libAvogadroQuantumIO.so.1
/usr/share/doc/avogadro
/usr/share/doc/avogadro/html
/usr/share/doc/avogadro/html/nav_h.png
/usr/share/doc/avogadro/html/index.html
/usr/share/doc/avogadro/html/sync_off.png
/usr/share/doc/avogadro/html/annotated.html
/usr/share/doc/avogadro/html/doxygen.css
/usr/share/doc/avogadro/html/class_avogadro_1_1_about_dialog.html
/usr/share/doc/avogadro/html/bdwn.png
/usr/share/doc/avogadro/html/class_avogadro_1_1_about_dialog-members.html
/usr/share/doc/avogadro/html/namespaces.html
/usr/share/doc/avogadro/html/sync_on.png
/usr/share/doc/avogadro/html/doc.png
/usr/share/doc/avogadro/html/class_avogadro_1_1_about_dialog.png
/usr/share/doc/avogadro/html/class_avogadro_1_1_application-members.html
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/usr/share/doc/avogadro/html/folderopen.png
/usr/share/doc/avogadro/html/open.png
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/usr/share/doc/avogadro/html/closed.png
/usr/share/doc/avogadro/html/dynsections.js
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/usr/share/doc/avogadro/html/class_avogadro_1_1_menu_builder.html
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/usr/share/doc/avogadro/html/functions_func.html
/usr/share/doc/avogadro/html/class_avogadro_1_1_background_file_format.png
/usr/share/doc/avogadro/html/jquery.js
/usr/share/doc/avogadro/html/class_avogadro_1_1_view_factory-members.html
/usr/share/doc/avogadro/html/class_avogadro_1_1_rpc_listener.png
/usr/share/doc/avogadro/html/tab_a.png
/usr/share/doc/avogadro/html/doxygen.png
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/var/lib/dpkg/info/avogadro.list
/var/lib/dpkg/info/libavogadro2-1:amd64.md5sums
/var/lib/dpkg/info/libavogadro2-1:amd64.shlibs
/var/lib/dpkg/info/python3-avogadro.prerm
/var/lib/dpkg/info/python3-avogadro.postinst
/var/lib/dpkg/info/libavogadro2-1:amd64.triggers
/var/lib/dpkg/info/avogadro.md5sums
/var/lib/dpkg/info/avogadro-utils.list
/var/lib/dpkg/info/python3-avogadro.md5sums
/var/lib/dpkg/info/libavogadro2-1:amd64.list
/var/lib/doc-base/documents/avogadro2
find: ‘/run/user/1000/gvfs’: Permissão negada
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    $\begingroup$ Same issue on a Windows install (besides that the plugin window doesn't display anything for me). I suppose you could post this as an issue on either the Avogadro 2 or the avogenerators repo. $\endgroup$ – Tyberius Sep 1 at 4:20
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    $\begingroup$ I can't help but feel like this will be a perfect one for Geoff Hutchinson. $\endgroup$ – Charlie Crown Sep 1 at 17:02
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    $\begingroup$ Geoff was last seen on 23 August, so he might be very busy with preparing for the upcoming academic year. If you need to get his attention, maybe you can send him a link to this question on his Twitter account: twitter.com/ghutchis. If you @StackMatter we can re-tweet it for you. $\endgroup$ – Nike Dattani Sep 6 at 2:08
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    $\begingroup$ The last few weeks have been pretty crazy with kids doing online school, etc. - but I definitely want to get the plugins in better shape, it's a much easier system to tweak and add new plugins. $\endgroup$ – Geoff Hutchison Sep 9 at 19:31
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    $\begingroup$ I had the same problem, and I resolved successfully by following installing from the source. $\endgroup$ – Gabriel Jara Oct 22 at 18:24
7
+100
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tldr; they need to be in certain directories to be found.

I don't know why the input generators were not part of the install package. Certainly on Mac, and AFAIK on Windows, they are and should be. On the other hand, Linux package maintainers often have rules about how they're supposed to handle such things and perhaps it's a separate package.

In Avogadro 2, we've made input generators and a bunch of other things into Python scripts. Basically, the script will pass some JSON to Avogadro to create a form (e.g., DFT functionals, basis sets, job types, etc.) and Avogadro passes JSON with the user options to the script.

This means in principle, users can easily add new generators, tweak the options, etc. with minimal coding. It also means updates can happen whenever, not just when we issue a release.

We're working on a plugin directory and better plugin installation (e.g., download or use git to grab plugins). I mean, doesn't every editor have plugins now?

The downloader has some known bugs, but it's been a busy start to the semester, unfortunately.

Avogadro will look in a few places for input generator scripts:

  • ${INSTALL_LIBRARY_DIR}/avogadro2/scripts/inputGenerators/
  • QStandardPaths::standardLocations(QStandardPaths::AppLocalDataLocation) + type

Generally on Linux, that might be:

  • /usr/local/lib/avogadro2/scripts/inputGenerators/
  • ~/.local/share/OpenChemistry/Avogadro/inputGenerators/
  • /usr/local/share/OpenChemistry/Avogadro/inputGenerators/
  • /usr/share/OpenChemistry/Avogadro/inputGenerators/

It's fairly easy to tweak the code to look at different directories, so please let me know in the comments.

On my Mac, I created a symlink from ~/Library/Application Support/OpenChemistry/Avogadro/inputGenerators to the git repository.

There's a definite need for a "please install this download for me" - and if anyone has a few hours, I'd happy help get that done. We can definitely use some help - lots of tasks are fairly quick.

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    $\begingroup$ We always welcome new contributors. I'll point out that we participate in Hacktoberfest, including easy things like tweaking functionals and basis sets, etc. github.com/OpenChemistry/avogenerators/blob/master/orca.py $\endgroup$ – Geoff Hutchison Sep 9 at 19:29
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    $\begingroup$ Is this for installing from source or the most recent binaries? Neither the Mac nor Windows binaries seem to have input generators besides GAMESS when I installed them. $\endgroup$ – Tyberius Sep 9 at 21:23
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    $\begingroup$ I test the Mac binaries routinely, and both 1.91 and the latest builds on GitHub have all the scripts. I'm pretty sure the Windows builds do too, although I see the GitHub builds are currently broken. Let's take this up on discuss.avogadro.cc $\endgroup$ – Geoff Hutchison Sep 9 at 21:30
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    $\begingroup$ @ksousa - the installer feature is currently broken. If you want to load in your home directory, you'd want ~/.local/share/OpenChemistry/Avogadro/inputGenerators/* - although it will look through subdirectories of that. $\endgroup$ – Geoff Hutchison Sep 10 at 1:45
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    $\begingroup$ @GeoffHutchison I made a post on the discussion forum: discuss.avogadro.cc/t/… $\endgroup$ – Tyberius Sep 10 at 20:34
3
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Workaround: Install the Windows port of old Avogadro under Linux, using Wine (tested under Mint 20).

Not a proper fix, but should get you going while this issue is sorted out by the developers and packagers. It's possible to install the standalone .exe version of the old Avogadro for Windows under Linux, using Wine. Wine is a compatibility layer, used by many people to run games under Linux, even if there is no Linux port for a given game. I tested it with Avogadro, and it worked.

  1. Install PlayOnLinux (graphical frontend for Wine).

In your terminal, input the following command:

sudo apt install playonlinux

The package manager should download about 140MB of the software and all prerequisites, so it may take a while.

  1. Download the Avogadro win32 executable at https://sourceforge.net/projects/avogadro/files/avogadro/1.2.0/

  2. Launch PlayOnLinux, click "install a program":

enter image description here

  1. Click "Install a non-listed program":

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  1. Read the prompts and click next until you reach the manual installation prompt:

enter image description here enter image description here enter image description here

  1. Select "Install a program in a new virtual drive". Click next:

enter image description here

  1. Input a name for the virtual drive where the software will be installed. I used just "avogadro", but you can use another name if you want:

enter image description here

  1. The next screen you can just leave as it is (checkboxes unmarked). Click next:

enter image description here

  1. Select "32 bits windows installation" (as the .exe version of Avogadro is compiled for a 32 bits environment). Click next:

enter image description here

  1. Wait a bit while PlayOnLinux creates your virtual driver, click next, and then browse for the .exe file you downloaded in step 2. Open it. Next:

enter image description here

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enter image description here

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  1. Now PlayOnLinux will run the Avogadro Setup Wizard. The steps here are the same you would do in a normal windows install. Just go through the wizard steps and accept the license agreement. The defaults in each prompt should be OK.

enter image description here

  1. When you reach the end of the installer wizard, and click finish, PlayOnLinux will ask you to choose a file to make a shortcut. Select Avogadro.exe, and click next:

enter image description here

  1. Now you can quit PlayOnLinux, and reboot your computer. After the reboot, you'll see the shortcut for old Avogadro under Wine in your desktop:

enter image description here

  1. Now you should be able to run the old Avogadro just by clicking the shortcut. It will render the graphics a bit slower, as it's running through the compatibility layer, but you will be able to keep using the input generators, and other functionality, while it gets ported to the Avogadro 2 from the repository:

enter image description here

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    $\begingroup$ I actually managed to install the old .deb of Avogadro 1.2 via GDebi on Mint 20, I just needed to uninstall certain packages and install certain packages, and then lock the version of package Avogadro in Synaptic. But obviously, now we can just use Geoff's answer. $\endgroup$ – Esmu Igors Oct 19 at 17:48
3
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I found in the Avogadro forum the solution to this problem. Compile the source code by following the simple instructions reported here: https://discuss.avogadro.cc/t/possible-issue-with-debian-ubuntu-packages-for-avogadro2-and-input-generators/3306.

I tried and it worked for me. It seems to be a bug with the packaging process.

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  • $\begingroup$ Nice. Thank You for pointing to those instructions. I just compiled it successfully. $\endgroup$ – ksousa Oct 18 at 16:43

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