Sorry to keep bugging with this… The latest nightly build (15-10-24), which included support for frequencies in MOLDEN format, now refuses to read the regular QChem frequencies when I start the app from Finder. (Yes, it reads MOLDEN when app is started from Finder.) For some reason, when I open Avogadro from the terminal, it is able to read both MOLDEN and QChem frequencies with no problem.
So, I am happy with being able to now being able to visualize my frequencies with Avogadro but figured I’d document this in case you’d like to fix it / another user runs into a similar situation.
Let me get this straight. If you launch the app and then open a Q-Chem output file, the frequencies don’t read. But if you launch from the terminal, you can read the Q-Chem frequencies?
If so, could you please send me the terminal output when you launch that way?
It sounds like an issue with the embedded Open Babel in that build.
This is the output when I open Avogadro from terminal and read the QChem output file. It opens the file just fine and reads the frequencies and intensities.
laptop:~ juanes$ avogadro
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"
Execution of PAC script at "http%3A%2F%2Fwpad%2Fwpad.dat" failed: The operation couldn’t be completed. (NSURLErrorDomain error -1002.)
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 15 2024 -- 17:39:45"
"Checking for energy scripts in path /Users/jearias/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"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/ani2x.py"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn1.py"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn2.py"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfnff.py"
registering GPL plugins
OBEnergy: method: MMFF94
OBEnergy: method: UFF
OBEnergy: method: GAFF
"Checking for commands scripts in path /Users/jearias/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/jearias/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"
"Checking for charges scripts in path /Users/jearias/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"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/antechamber.py"
"Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/xtb.py"
"Checking for formatScripts scripts in path /Users/jearias/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"
qt.qpa.fonts: Populating font family aliases took 125 ms. Replace uses of missing font family "Inter" with one that exists to avoid this cost.
OBEnergy: method: MMFF94
2024-10-16 15:20:51.877 Avogadro2[47810:2081825] 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" "-ilog /Users/jearias/Desktop/Cofin/CO2/CO2_Freq_QChem.out -ocjson"
Not too sure how I can generate the analogous log when launching Avogadro “normally”. It is able to read the file but not the frequencies.
The recent builds use an not-yet-released beta version of Open Babel with CJSON support. If Avogadro can’t find CJSON support, it falls back to CML which doesn’t have vibrations.
One quick workaround is to install cclib in your environment and the cclib Avogadro plugin as mentioned above.
Avogadro should try cclib over Open Babel if the plugin is installed.
If you don’t have obabel installed in your path, I don’t know. I’ll have to think how you can get the console log when you launch from the Finder.
Here is the output after following your steps. Only the output for process “Avogadro2” (there are other outputs from kernel and other things - happy to provide them if they are useful).
default 16:40:37.936701-0600 Avogadro2 [0x6000021cc000] activating connection: mach=true listener=false peer=false name=com.apple.cfprefsd.daemon
default 16:40:37.936769-0600 Avogadro2 [0x6000021cc0f0] activating connection: mach=true listener=false peer=false name=com.apple.cfprefsd.agent
default 16:40:37.957206-0600 Avogadro2 [0x6000021c8e10] activating connection: mach=true listener=false peer=false name=com.apple.distributed_notifications@Uv3
default 16:40:37.958466-0600 Avogadro2 No persisted cache on this platform.
default 16:40:37.959743-0600 Avogadro2 [0x6000021c8f00] activating connection: mach=true listener=false peer=false name=com.apple.tccd.system
default 16:40:37.967324-0600 Avogadro2 [0x6000021c8f00] invalidated after the last release of the connection object
default 16:40:37.967540-0600 Avogadro2 server port 0x00002e0f, session port 0x00002e0f
default 16:40:37.978126-0600 Avogadro2 [0x6000021c00f0] activating connection: mach=true listener=false peer=false name=com.apple.coreservices.launchservicesd
default 16:40:37.978660-0600 Avogadro2 [0x6000021c4c30] activating connection: mach=true listener=false peer=false name=com.apple.analyticsd
default 16:40:37.980184-0600 Avogadro2 New connection 0x95513 main
default 16:40:37.980186-0600 Avogadro2 Received configuration update from daemon (initial)
default 16:40:37.980309-0600 Avogadro2 Current system appearance, (HLTB: 2), (SLS: 1)
default 16:40:37.980593-0600 Avogadro2 Current system appearance, (HLTB: 2), (SLS: 1)
default 16:40:37.981003-0600 Avogadro2 Post-registration system appearance: (HLTB: 2)
default 16:40:37.981331-0600 Avogadro2 [0x6000021cc3c0] activating connection: mach=true listener=false peer=false name=com.apple.pasteboard.1
default 16:40:37.986171-0600 Avogadro2 [0x7fc9a6704080] activating connection: mach=true listener=false peer=false name=com.apple.lsd.mapdb
default 16:40:38.000349-0600 Avogadro2 CHECKIN: pid=49779
default 16:40:38.007200-0600 Avogadro2 CHECKEDIN: pid=49779 asn=0x0-0x1b2ab29 foreground=1
default 16:40:38.007455-0600 Avogadro2 [0x7fc9a700a430] activating connection: mach=false listener=true peer=false name=(anonymous)
default 16:40:38.007467-0600 Avogadro2 [0x7fc9a700a430] Channel could not return listener port.
default 16:40:38.008085-0600 Avogadro2 [0x7fc9a71291f0] activating connection: mach=false listener=false peer=true name=com.apple.xpc.anonymous.0x7fc9a700a430.peer[353].0x7fc9a71291f0
default 16:40:38.010354-0600 Avogadro2 FRONTLOGGING: version 1
default 16:40:38.010410-0600 Avogadro2 Registered, pid=49779 ASN=0x0,0x1b2ab29
default 16:40:38.012861-0600 Avogadro2 [0x7fc9a700a430] Channel could not return listener port.
default 16:40:38.017623-0600 Avogadro2 BringForward: pid=49779 asn=0x0-0x1b2ab29 bringForward=1 foreground=1 uiElement=0 launchedByLS=1 modifiersCount=1 allDisabled=0
default 16:40:38.018893-0600 Avogadro2 BringFrontModifier: pid=49779 asn=0x0-0x1b2ab29 Modifier 0 hideAfter=0 hideOthers=0 dontMakeFrontmost=0 mouseDown=0/0 seed=0/0
default 16:40:38.020095-0600 Avogadro2 BringForward: pid=49779 asn=0x0-0x1b2ab29
default 16:40:38.020376-0600 Avogadro2 SetFrontProcess: asn=0x0-0x1b2ab29 options=0
default 16:40:38.037547-0600 Avogadro2 [0x7fc9a700a430] Channel could not return listener port.
default 16:40:38.040947-0600 Avogadro2 [0x7fc9a700a430] Channel could not return listener port.
default 16:40:38.055350-0600 Avogadro2 [0x7fc9a71369c0] activating connection: mach=false listener=false peer=false name=com.apple.carboncore.csnameddata
default 16:40:38.060211-0600 Avogadro2 [0x6000022c0900] activating connection: mach=true listener=false peer=false name=com.apple.fonts
default 16:40:38.082942-0600 Avogadro2 [0x6000021c5b30] activating connection: mach=true listener=false peer=false name=com.apple.cvmsServ
default 16:40:38.146779-0600 Avogadro2 networkd_settings_read_from_file initialized networkd settings by reading plist directly
default 16:40:38.146913-0600 Avogadro2 networkd_settings_read_from_file initialized networkd settings by reading plist directly
default 16:40:38.147485-0600 Avogadro2 TrustSettingsUseXPC is enabled (via feature flags)
default 16:40:38.147531-0600 Avogadro2 Enabling System Keychain Always due to platform
default 16:40:38.147640-0600 Avogadro2 [0x6000021d4000] activating connection: mach=true listener=false peer=false name=com.apple.trustd.agent
default 16:40:38.154560-0600 Avogadro2 Recording an MDS plugin: /System/Library/Security/ldapdl.bundle {87191ca6-0fc9-11d4-849a-000502b52122}
default 16:40:38.155035-0600 Avogadro2 Recording an MDS plugin: /System/Library/Frameworks/Security.framework {87191ca0-0fc9-11d4-849a-000502b52122}
default 16:40:38.414680-0600 Avogadro2 [0x6000021c03c0] activating connection: mach=true listener=false peer=false name=com.apple.cfnetwork.cfnetworkagent
default 16:40:38.414767-0600 Avogadro2 Sending CFNA PAC query
default 16:40:38.416110-0600 Avogadro2 Received CFNA PAC response
default 16:40:38.417102-0600 Avogadro2 Execution of PAC script at "http%3A%2F%2Fwpad%2Fwpad.dat" failed: The operation couldn’t be completed. (NSURLErrorDomain error -1002.)
default 16:40:38.422235-0600 Avogadro2 nw_path_libinfo_path_check [79A11C69-E311-478B-A26C-3376805861C0 Hostname#cfbfb974:0 tcp, legacy-socket, attribution: developer]
libinfo check path: satisfied (Path is satisfied), interface: utun4, ipv4, ipv6, dns, proxy
default 16:40:38.448398-0600 Avogadro2 nw_path_evaluator_start [18085F48-A61A-4C3B-A466-26ACEF3922B8 IPv4#f0e9b34c:0 generic, local: 10.79.130.67:0, attribution: developer]
path: satisfied (Path is satisfied), interface: utun4, scoped, ipv4, ipv6, dns, proxy
default 16:40:38.528491-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/ani2x.py"
default 16:40:38.587466-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn1.py"
default 16:40:38.638111-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfn2.py"
default 16:40:38.694890-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/energy/gfnff.py"
default 16:40:39.504738-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/antechamber.py"
default 16:40:39.558732-0600 Avogadro2 "Cannot load script /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/charges/xtb.py"
default 16:40:39.873055-0600 Avogadro2 Populating font family aliases took 129 ms. Replace uses of missing font family "Inter" with one that exists to avoid this cost.
default 16:40:39.910465-0600 Avogadro2 NSApp cache appearance:
-NSRequiresAquaSystemAppearance: 0
-appearance: (null)
-effectiveAppearance: <NSCompositeAppearance: 0x6000030c1900
(
"<NSDarkAquaAppearance: 0x6000030c1a00>",
"<NSSystemAppearance: 0x6000030c0180>"
)>
default 16:40:39.917201-0600 Avogadro2 [0x7fc976a35970] activating connection: mach=true listener=false peer=false name=com.apple.windowmanager.server
default 16:40:39.923784-0600 Avogadro2 [0x6000021c5ef0] activating connection: mach=true listener=false peer=false name=com.apple.dock.fullscreen
default 16:40:40.058176-0600 Avogadro2 [0x7fc976a337f0] activating connection: mach=true listener=false peer=false name=com.apple.iconservices
default 16:40:40.059250-0600 Avogadro2 [0x7fc9a7247350] activating connection: mach=true listener=false peer=false name=com.apple.iconservices.store
default 16:40:40.065887-0600 Avogadro2 order window front conditionally: 3531 related: 0
default 16:40:40.067426-0600 Avogadro2 Registering for test daemon availability notify post.
default 16:40:40.067538-0600 Avogadro2 notify_get_state check indicated test daemon not ready.
default 16:40:40.067611-0600 Avogadro2 notify_get_state check indicated test daemon not ready.
default 16:40:40.067681-0600 Avogadro2 notify_get_state check indicated test daemon not ready.
default 16:40:40.069902-0600 Avogadro2 [0x6000021e62b0] activating connection: mach=true listener=false peer=false name=com.apple.coreservices.appleevents
default 16:40:40.070538-0600 Avogadro2 [0x7fc9a700a430] Channel could not return listener port.
default 16:40:40.070934-0600 Avogadro2 SignalReady: pid=49779 asn=0x0-0x1b2ab29
default 16:40:40.071700-0600 Avogadro2 SIGNAL: pid=49779 asn=0x0x-0x1b2ab29
default 16:40:40.103971-0600 Avogadro2 Pixel format registry initialized. Constant classes enabled.
default 16:40:40.137511-0600 Avogadro2 [0x6000021d1860] activating connection: mach=false listener=false peer=false name=com.apple.ViewBridgeAuxiliary
default 16:40:40.137727-0600 Avogadro2 [0x7fc9a7218200] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:40.138155-0600 Avogadro2 [0x7fc9a7016e80] activating connection: mach=false listener=true peer=false name=(anonymous)
default 16:40:40.138164-0600 Avogadro2 [0x7fc9a7016e80] Channel could not return listener port.
default 16:40:40.138674-0600 Avogadro2 [0x6000021c5a40] activating connection: mach=false listener=false peer=false name=com.apple.TextInputUI.xpc.CursorUIViewService
default 16:40:40.138922-0600 Avogadro2 [0x6000021c5a40] invalidated after the last release of the connection object
default 16:40:40.139151-0600 Avogadro2 [0x6000021d1860] invalidated after the last release of the connection object
default 16:40:40.139520-0600 Avogadro2 Initializing connection
default 16:40:40.139560-0600 Avogadro2 Removing all cached process handles
default 16:40:40.139590-0600 Avogadro2 Sending handshake request attempt #1 to server
default 16:40:40.139601-0600 Avogadro2 Creating connection to com.apple.runningboard
default 16:40:40.139612-0600 Avogadro2 [0x6000021e6d00] activating connection: mach=true listener=false peer=false name=com.apple.runningboard
default 16:40:40.140279-0600 Avogadro2 Gained inheritances: {(
<RBSInheritance| environment:(none) name:com.apple.launchservices.userfacing origID:386-353-128148 0>
)}
default 16:40:40.140330-0600 Avogadro2 Handshake succeeded
default 16:40:40.140347-0600 Avogadro2 Identity resolved as app<application.cc.avogadro.7640654.7641185(146596)>
default 16:40:40.141942-0600 Avogadro2 [0x7fc9a7221e20] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:40.141994-0600 Avogadro2 [0x6000021d1860] activating connection: mach=false listener=false peer=false name=com.apple.ViewBridgeAuxiliary
default 16:40:40.142168-0600 Avogadro2 [0x7fc976a43d10] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:40.142241-0600 Avogadro2 [0x6000021d1860] invalidated after the last release of the connection object
default 16:40:40.161031-0600 Avogadro2 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:.
default 16:40:40.165026-0600 Avogadro2 [0x6000021c2490] activating connection: mach=true listener=false peer=false name=com.apple.window_proxies
default 16:40:40.165126-0600 Avogadro2 [0x6000021c2490] invalidated because the current process cancelled the connection by calling xpc_connection_cancel()
default 16:40:40.169348-0600 Avogadro2 Gained inheritances: {(
<RBSInheritance| environment:(none) name:com.apple.frontboard.visibility origID:386-381-128157 0>
)}
default 16:40:40.170555-0600 Avogadro2 order window front conditionally: 3531 related: 0
default 16:40:40.170876-0600 Avogadro2 window TUINSWindow 3533 finishing close
default 16:40:40.170998-0600 Avogadro2 order window: 3533 op: 0 relative: 0 related: 0
default 16:40:40.171966-0600 Avogadro2 [0x6000021e6df0] activating connection: mach=false listener=false peer=false name=com.apple.TextInputUI.xpc.CursorUIViewService
default 16:40:40.172194-0600 Avogadro2 [0x6000021e6df0] invalidated after the last release of the connection object
default 16:40:40.172549-0600 Avogadro2 [0x7fc9a71421a0] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:40.172590-0600 Avogadro2 [0x7fc976a6fb40] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:40.172873-0600 Avogadro2 -[TUINSCursorUIController activate:]_block_invoke: Create CursorUIViewService: TUINSRemoteViewController
default 16:40:40.176242-0600 Avogadro2 void _updateToReflectAutomaticTerminationState(void) Setting _kLSApplicationWouldBeTerminatedByTALKey=0
default 16:40:40.212491-0600 Avogadro2 -[TUINSCursorUIController activate:]_block_invoke: Create CursorUIViewService: TUINSRemoteViewController
default 16:40:40.212742-0600 Avogadro2 [0x7fc976a43d10] invalidated because the current process cancelled the connection by calling xpc_connection_cancel()
default 16:40:40.212757-0600 Avogadro2 [0x7fc9a7221e20] invalidated because the current process cancelled the connection by calling xpc_connection_cancel()
fault 16:40:40.212990-0600 Avogadro2 CLIENT ERROR: TUINSRemoteViewController does not override -<private> and thus cannot react to catastrophic errors beyond logging them
default 16:40:40.278650-0600 Avogadro2 [0x6000021e1e00] activating connection: mach=false listener=false peer=false name=com.apple.hiservices-xpcservice
default 16:40:43.978616-0600 Avogadro2 Window QNSPanel 0x7fc9769056e0 ordered front from a non-active application and may order beneath the active application's windows.
default 16:40:43.978653-0600 Avogadro2 order window front conditionally: 353c related: 0
default 16:40:44.106554-0600 Avogadro2 order window: 353c op: 0 relative: 0 related: 0
default 16:40:44.111654-0600 Avogadro2 window QNSPanel 353c finishing close
default 16:40:44.111768-0600 Avogadro2 order window: 353c op: 0 relative: 0 related: 0
error 16:40:45.225841-0600 Avogadro2 BOOL _NSPersistentUIDeleteItemAtFileURL(NSURL *const __strong) Failed to stat item: <private>
default 16:40:47.284001-0600 Avogadro2 Gained inheritances: {(
<RBSInheritance| environment:(none) name:com.apple.launchservices.userfacing origID:386-353-128158 0>,
<RBSInheritance| environment:(none) name:com.apple.launchservices.userfacing origID:386-353-128158 0>
)}
default 16:40:47.284734-0600 Avogadro2 Gained inheritances: {(
<RBSInheritance| environment:(none) name:com.apple.frontboard.visibility origID:386-381-128159 0>
)}
default 16:40:47.306221-0600 Avogadro2 [0x6000021e1ef0] activating connection: mach=false listener=false peer=false name=com.apple.TextInputUI.xpc.CursorUIViewService
default 16:40:47.306703-0600 Avogadro2 [0x6000021e1ef0] invalidated after the last release of the connection object
default 16:40:47.355807-0600 Avogadro2 [0x7fc9a724e590] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:47.355874-0600 Avogadro2 [0x7fc9a71488a0] activating connection: mach=false listener=false peer=false name=(anonymous)
default 16:40:47.373286-0600 Avogadro2 -[TUINSCursorUIController activate:]_block_invoke: Create CursorUIViewService: TUINSRemoteViewController
default 16:40:47.373601-0600 Avogadro2 [0x7fc976a6fb40] invalidated because the current process cancelled the connection by calling xpc_connection_cancel()
default 16:40:47.373620-0600 Avogadro2 [0x7fc9a71421a0] invalidated because the current process cancelled the connection by calling xpc_connection_cancel()
fault 16:40:47.373802-0600 Avogadro2 CLIENT ERROR: TUINSRemoteViewController does not override -<private> and thus cannot react to catastrophic errors beyond logging them
default 16:40:47.406198-0600 Avogadro2 -[TUINSCursorUIController scheduleUpdateCursorLocation]
In doing this exercise to produce this logs, I have realized that Avogadro seems to be able to read the QChem frequencies in “random launches” from Finder. I mean that some times when I open from Finder it reads fine and some times it does not.
Got it, it works. Not too sure if that version I installed with pipx was ever hooked up to Avogadro but I’m assuming the one I downloaded directly with the functionality available in Avogadro seems to work. I gave it a few tries and now it seems to open QChem frequencies without randomly not working.
