Avogadro 1.99.0 Unable to Calculate Energy

yjin27 · October 13, 2024, 4:37pm

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.99.0
Operating system and version: MacOS Sonoma 14.5

Expected Behavior

Extensions → Calculate → Energy giving the formation energy of a molecule constructed

Actual Behavior

With any molecule in any force field, the energy calculation always returns 0 (and so is the force norm), regardless of geometry optimizations.

ghutchis · October 13, 2024, 5:07pm

Please try a nightly build from https://two.avogadro.cc/

yjin27 · October 13, 2024, 6:40pm

Hi, I downloaded the nightly build (intel) and it’s still the same, showing MMFF94 energy = 0 for any molecule I put in.

ghutchis · October 15, 2024, 1:18am

I see there’s also a recent bug report about this:

github.com/OpenChemistry/avogadrolibs

Energy and Forces Calculation not Working on Mac

opened 03:08AM - 03 Oct 24 UTC

ChemEm

**Avogadro version: 1.99.0** - Avogadrolibs: 1.99.0 - Qt: 5.15.8 **Deskto…p version:** - OS: MacOS - Version: 13.5.1 - Compiler: N/A **Describe the bug** Energy and forces calculation under "Extensions"-->"Calculate" always returns 0, even after configuring and optimizing the geometry through Babel. **To Reproduce** Steps to reproduce the behavior: 1. Go to 'Extensions' 2. Click on 'Calculate' 3. Select 'Energy' or 'Forces' 4. See error, display is 'MMFF94 Energy = 0' **Expected behavior** The error should not be 0, and should display units. **Screenshots** <img width="676" alt="Screenshot 2024-10-02 at 22 08 07" src="https://github.com/user-attachments/assets/7f6e13a4-dc06-4295-b060-9b64ca0d0bd0"> **Additional context** Just using this to see the energy of different butane conformers.

Would you be willing to run from the Terminal.app - this will show the console messages and hopefully give me more information about what’s going on.

If you open up a Terminal, you can run Avogadro2 like this:

/Applications/Avogadro2.app/Contents/MacOS/Avogadro2

(This assumes you’ve installed Avogadro in your /Applications folder.)

You’ll see a whole bunch of messages like:

Using locale:  "en_US"
qt.network.ssl: Error receiving trust for a CA certificate
Extension plugins dynamically found… 49
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats read"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats write"
… (etc)

Use the app - draw a molecule, etc. and then calculate the energy or optimize and copy / paste the log here.

I’d like to know why you’re not seeing any energies (but on my MacBook and other test Macs it’s working fine.)

yjin27 · October 15, 2024, 2:57am

Hi, this is what I got from the terminal: It seems that some files are not found, but I’m not entirely sure what they mean:

Error: Failed to open library “/Library/Frameworks/3DconnexionNavlib.framework/3DconnexionNavlib”! Error: dlopen(/Library/Frameworks/3DconnexionNavlib.framework/3DconnexionNavlib, 0x0005): tried: ‘/Library/Frameworks/3DconnexionNavlib.framework/3DconnexionNavlib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/3DconnexionNavlib.framework/3DconnexionNavlib’ (no such file), ‘/Library/Frameworks/3DconnexionNavlib.framework/3DconnexionNavlib’ (no such file)!

Using locale: “en_US”

Extension plugins dynamically found… 49

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-L formats read”

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-L formats write”

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-L forcefields”

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-L charges”

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-V”

“/Applications/Avogadro2.app/Contents/MacOS/obabel” found: “/Applications/Avogadro2.app/Contents/MacOS/obabel: Open Babel 3.1.1 – Oct 12 2024 – 00:12:51”

“Checking for energy scripts in path /Users/yuchengjin/Library/Application Support/OpenChemistry/Avogadro/energy”

“Checking for energy scripts in path /Library/Application Support/OpenChemistry/Avogadro/energy”

“Checking for energy scripts in path /Applications/Avogadro2.app/Contents/Resources/energy”

“Checking for energy scripts in path /Applications/Avogadro2.app/Contents/MacOS/…/lib/avogadro2/scripts/energy”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/ani2x.py”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn1.py”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn2.py”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfnff.py”

registering GPL plugins

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

OBEnergy: method: MMFF94

OBEnergy: method not found: MMFF94

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:

ops

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

OBEnergy: method: UFF

OBEnergy: method not found: UFF

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:

ops

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

OBEnergy: method: GAFF

OBEnergy: method not found: GAFF

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:

ops

“Checking for commands scripts in path /Users/yuchengjin/Library/Application Support/OpenChemistry/Avogadro/commands”

“Checking for commands scripts in path /Library/Application Support/OpenChemistry/Avogadro/commands”

“Checking for commands scripts in path /Applications/Avogadro2.app/Contents/Resources/commands”

“Checking for commands scripts in path /Applications/Avogadro2.app/Contents/MacOS/…/lib/avogadro2/scripts/commands”

“Checking for inputGenerators scripts in path /Users/yuchengjin/Library/Application Support/OpenChemistry/Avogadro/inputGenerators”

“Checking for inputGenerators scripts in path /Library/Application Support/OpenChemistry/Avogadro/inputGenerators”

“Checking for inputGenerators scripts in path /Applications/Avogadro2.app/Contents/Resources/inputGenerators”

“Checking for inputGenerators scripts in path /Applications/Avogadro2.app/Contents/MacOS/…/lib/avogadro2/scripts/inputGenerators”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Checking for charges scripts in path /Users/yuchengjin/Library/Application Support/OpenChemistry/Avogadro/charges”

“Checking for charges scripts in path /Library/Application Support/OpenChemistry/Avogadro/charges”

“Checking for charges scripts in path /Applications/Avogadro2.app/Contents/Resources/charges”

“Checking for charges scripts in path /Applications/Avogadro2.app/Contents/MacOS/…/lib/avogadro2/scripts/charges”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/antechamber.py”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

“Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/xtb.py”

“Checking for formatScripts scripts in path /Users/yuchengjin/Library/Application Support/OpenChemistry/Avogadro/formatScripts”

“Checking for formatScripts scripts in path /Library/Application Support/OpenChemistry/Avogadro/formatScripts”

“Checking for formatScripts scripts in path /Applications/Avogadro2.app/Contents/Resources/formatScripts”

“Checking for formatScripts scripts in path /Applications/Avogadro2.app/Contents/MacOS/…/lib/avogadro2/scripts/formatScripts”

Python interpreter “/Users/runner/hostedtoolcache/Python/3.11.9/x64/bin/python3” does not exist trying “python” in your path. Please set a path to the python interpreter.

qt.qpa.fonts: Populating font family aliases took 139 ms. Replace uses of missing font family “Inter” with one that exists to avoid this cost.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

OBEnergy: method: MMFF94

OBEnergy: method not found: MMFF94

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:

ops

2024-10-14 21:53:26.369 Avogadro2[70255:24499744] WARNING: Secure coding is automatically enabled for restorable state! However, not on all supported macOS versions of this application. Opt-in to secure coding explicitly by implementing NSApplicationDelegate.applicationSupportsSecureRestorableState:.

Setting default format to cjson

Open Babel formats ready: 146

OBProcess::executeObabel: Running “/Applications/Avogadro2.app/Contents/MacOS/obabel” “-icjson -ocjson --minimize --noh --log --crit 1e-06 --ff UFF --steps 2500 --rvdw 10 --rele 10 --freq 10”

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

==============================

*** Open Babel Error in LoadAllPlugins

Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.

////
Thanks for checking this!

ghutchis · October 15, 2024, 3:12am

That’s the key problem. It should be setting this on launch so it can find the integrated Open Babel … but clearly that’s not working.

I’ll take a look tomorrow and see if I can sort that out.

ghutchis · October 15, 2024, 4:34pm

Could you take a look at this build?

github.com/OpenChemistry/avogadrolibs

Try adding BABEL_LIBDIR and BABEL_DATADIR to environment

OpenChemistry:master ← ghutchis:add-mac-babel-environment

opened 03:49AM - 15 Oct 24 UTC

ghutchis

+9 -0

Should fix #1723 Developer Certificate of Origin Version 1.1 Copyright (C…) 2004, 2006 The Linux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.

There’s a link to a MacOS DMG:
https://github.com/OpenChemistry/avogadrolibs/suites/29619884679/artifacts/2056163545

yjin27 · October 15, 2024, 5:12pm

I cannot open the downloaded app

yjin27 · October 15, 2024, 5:18pm

Never mind I changed the setting, and it worked!! It seems like all functions that require Open Babel now work. Thank you a lot!

ghutchis · October 15, 2024, 5:30pm

Yeah, it’s unsigned, but you can still open it. Control-click to open it again, and you’ll have the option to open anyway.

Signed binaries can only be produced on GitHub once a change is accepted (e.g., the nightly binaries). This is a security thing – it prevents anyone else from having access to the official signing information.

system · October 18, 2024, 5:30pm

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