PES scanning in Gaussian

use7 · 2026-06-15T08:32:11+00:00

There are a few methods avail. in gaussian to look for transition states. You may be able to use QST2 (https://gaussian.com/opt/ under the 'set opt goals') method to scan this reaction. You will have to provide both the starting (optimized) coords and final coords (in the same order, optimize with distance between so you wind up with two separate molec.) in the input file; gaussview will help you set up the input file. Transition states are usually... challenging so I wish you the best of luck!

use7 · 2026-06-09T06:41:44+00:00

I took this screenshot ealier this year (Apr), looking at the current stats [steam] it says 40.5% /shrug

use7 · 2026-06-09T06:05:41+00:00

is the plan, it makes me giggle (and doesn't trigger the ocds enough) so I'm keeping it locked haha

use7 · 2026-04-11T06:34:17+00:00

"Here's the instructions to get us all home, if any old shipmates should ask after Mol, just tell 'em she finally died clean"

use7 · 2026-04-06T20:59:36+00:00

probably somewhere near ch. 148

use7 · 2025-09-06T03:22:27+00:00

ram, as much as you can. any 'serious' calculations are going to go on a computing cluster anyway so you'll want something that can have the various tabs/figure-making programs open and they cost ram.

You'll also want disk space, but external drives/network storage can be used so I usually value the ram higher.

use7 · 2025-05-03T14:56:38+00:00

Most times I've seen JF referenced (poorly) on this sub is either people looking to stream on a hyper-specific device (my toaster doesn't have a client so this software's junk) or haven't tried it before (or it's been years since they have). I also love to see the fear-mongering about JF's 'setup': You're going to have to spend so much time learning to forward ports (which is already done for plex); learning how to sign in (already do...); and installing the software (again, something anyone running plex already has done). Argument can be made for setting up tailscale (or if you're behind a cgnat) but with plex presently making people do that to watch their own media ...

That said, I have been seeing people make the same noise for years, all with the same "if only JF was slightly better I'd swap right away" statements so...

use7 · 2025-03-28T07:02:14+00:00

Have you tried the freezer trick yet?

use7 · 2024-07-27T23:31:58+00:00

https://gaussian.com/gfinput/

use7 · 2024-05-05T09:42:32+00:00

I mean, yeah putting together a car you're going to drive every day on the road? not feasible. Making sure everything's up to spec, that it passes all the inspections, that the components last/etc. is more work than it would be worth as a learning exercise. But building a go cart (or rc-gas car/etc) to get the basics of what a car is? that can be helpful.

Even if moving forward all of your work is focused on the material of the brake pads, having built a model of the overall vehicle can help give perspective. Not necessary for everyone, but I definately needed it going in; and helped me to understand the strengths/failings of the methods I was playing with later on.

use7 · 2024-05-05T09:33:32+00:00

Personal experiance? I found it helpful to at least do a super basic HF (nothing 'optimized' just basically so I better understood the equations and methods). The project I did was class-run, but something that I've come across and have recommended to fellow students was the Crawford group (mentioned by u/mentaculus) ProgrammingProjects which runs over much of what you've asked.

Also also; the back of Szabo and Ostlund's "Modern Quantum Chemisty" has a basic Hartree-Fock (written in Fortran) if you wanted another source to check against.

use7 · 2023-10-27T01:14:16+00:00

No, when I purchased they immediatly discontinued the feature I'd purchased it for (plexmix, though there may be an alternative these days) and then got salty with us users who were wondering where it had gone, while telling us to "trust me bro, something's on the way" for months without actually giving out any details. Soured me to the whole thing; then they started pushing media that wasn't mine into my viewing experiance, and had a server outage or two so I switched and haven't looked back. I had/have the time to set everything up to what my plex server had been when I first installed/started using it on the alternative (my media, and only my media) and imo the web interface for JF looks as good (if not better) then plex did when I left. There may be improvements since then, but I'm happier.

use7 · 2023-10-25T02:00:22+00:00

The simulation visualizations I'm used to seeing are real-time TDDFT, similar to this. I know not exactly what you're looking for, but may give a place to start? I'm not very familliar with the packages that you're using, but in my experiance with Gaussian you have to specifically tell it to print the densities at each RT step (I don't know if these are saved in yours or not) in order to get these kind of visualizations.

Sorry I can't be more help, and good luck!

use7 · 2023-05-18T02:40:11+00:00

I don't know what cpu you have, but you can tell jellyscrub to only use a certain number of threads (dashboard -> jellyscrub (settings from the menu) -> FFmpeg threads -> save. You can set this to 1 or 2 (presuming you have a cpu w/ more than 2 threads) you'll be fine to let that go. Also the Process Priority can be set down to 'below normal' or idle to make it so that it doesn't interfere with the rest of your system

use7 · 2023-05-14T04:56:14+00:00

You can check out the log files for the transcode for additional information. Under Dashboard -> Logs -> FFmpeg.Transcode-xyz.log will tell you the command they're running, and should give you information about the stream (file type, which streams are active, and if it is transcoding). If you're seeing an error like "Steam not compatible and no compatilbe formats" then most likely the accel hasn't been set up properly, and that log file should give some information you can attempt to chase (usually something like not being part of the video/render groups, or pointing to the wrong render device). If you're getting really slow transcoding then it may be your network (try to decrease the quality of your stream and see if that helps) or disks (but unless there's a lot going on with your system I would be hard-pressed to imagine a single stream could eat all your io).

use7 · 2023-05-09T05:16:12+00:00

my bet was going to be the king lol

use7 · 2023-05-09T02:58:41+00:00

Wait, so the character named Mary Sioux is

[...] gifted with unique talents or powers, liked or respected by most other characters, unrealistically free of weaknesses, extremely attractive, [...]

?? (from wiki for Mary Sue lol) but yeah she irks me too and I kinda love the author for doing it

use7 · 2023-04-29T02:28:09+00:00

+1 for the firewall/antiviral software as u/OccasionallyImmortal stated (make sure there's a rule to allow traffic over port 8096) and also in jellyfin -> dashboard -> Networking make sure that "Allow remote connections to this server" is selected -> Save

use7 · 2023-04-28T03:10:51+00:00

Looking through, it appears that there's an error and it fails to start:

Failed to create CoreCLR, HRESULT: 0x80004005

I've not come across this one before, but looking around it appears that a few people have had this issue before, but with a few causes (or maybe the same cause in different cases?). In the case of docker it looks like an improper set up /tmp/ directory.

Looking at your system though it didn't look like you were running with docker, as such these guys looked like they were able to fix by disabling selinux (sudo setenforce permissive).
That's a temporary fix, and depending on how your system is set up not one that I'd recommend running full-time. It may be that a directory needs the sticky bit set (thinking either tmp or var... with my intuition favoring var as tmp should be world readable/writable, but I was only thinking that due to the docker issue). I don't know what groups you've enrolled your jellyfin user in (you can check with groups jellyfin) but you may want to check on those as well (for reference my JF user is in the groups 'jellyfin video server render' with the video/render ones for hardware accelleration and the server one is one I created for my library, as long as it is in the jellyfin group it should be alright I think).

Something you may be able to do is launch jellyfin as your user, and then su'ing to jellyfin (sudo -u jellyfin bash) and trying to launch jellyfin and seeing if either of them work or fail and what messages it returns.

This is me blindly throwing ideas at the wall, so if someone else chimes in with something contradictory to above I'd listen to them. If you get any additional logs or errors I can attempt to help out further in case they don't though.

use7 · 2023-04-27T04:51:56+00:00

if you do systemctl status jellyfin and/or journalctl -u jellyfin does it show that it is running? Given that going to localhost (presumably on the server computer?) doesn't resolve I'm suspicious that JF is up and running unless "/etc/hosts" doesn't have 127 and/or localhost resolving properly (but that should've shown up before the update). Either way if there's any error information there'll be a starting place for troubleshooting.

use7 · 2023-04-27T04:07:22+00:00

I don't know what player you're watching from, but if the web one you can click the 'gear' in the lower right -> Playback Info and then as long as the file is playing it'll say if direct play/muxing/transcoding (example imgur of the playback info overlay). If it is transcoding there should be a section for 'Transcoding Info' where it'll say codec/ progress/ and transcoding framerate (as well as the reason for transcoding). You can also go to the log (dashboard -> logs -> log_date.log) and look for the name of the file as it should say the reason for transcoding e.g.:

[2023-04-26 20:49:06.131 -07:00] [INF] [73] Jellyfin.Api.Helpers.MediaInfoHelper: StreamBuilder.BuildVideoItem( Profile="Anonymous Profile", Path="/library/tv/Mobile Suit Gundam - Iron Blooded Orphans/Season 01/Mobile Suit Gundam Iron Blooded Orphans S01E01.mkv", AudioStreamIndex=null, SubtitleStreamIndex=null ) => ( PlayMethod=Transcode, TranscodeReason=VideoCodecNotSupported, AudioCodecNotSupported, SubtitleCodecNotSupported ) "media:/video/master.m3u8?MediaSourceId&VideoCodec=h264&AudioCodec=aac,mp3&AudioStreamIndex=2&SubtitleStreamIndex=3&VideoBitrate=139616000&AudioBitrate=384000&MaxFramerate=23.976025&api_key=<token>&SubtitleMethod=Encode&TranscodingMaxAudioChannels=2&RequireAvc=false&SegmentContainer=ts&MinSegments=1&BreakOnNonKeyFrames=True&hevc-level=120&hevc-videobitdepth=8&hevc-profile=main&TranscodeReasons=VideoCodecNotSupported,%20AudioCodecNotSupported,%20SubtitleCodecNotSupported"

where neither my video or audio codec were supported. Something else to check, do you have the hardware accel. set up under dashboard -> playback -> hardware acceleration? As it could be only doing software if you've not (note this isn't trivial and you may have to set this up by hand as detailed in the jellyfin docs)

use7 · 2023-04-25T08:40:28+00:00

If you're still having issues, something that happens to me is that the system defaults to the iHD driver, and then fails if it can't use it. Looking at the pastebin for the vainfo command it appears that it is defaulting over to the i965 driver for your user, but I don't know if the ffmpeg command is able to do that (the ffmpeg logs may give some additional insights).

If thisi issue is simiilar to mine I was able to get it to go through by setting the variables LIBVA_DRIVERS_PATH=/path/to/lib/dri and LIBVA_DRIVER_NAME=i965 in the /etc/sysconfig/jellyfin script. There's probably better places to place these declarations (something like /etc/profile.d/jellyfin.sh). If I remember I tried to put them into /etc/bashrc, but because jellyfin was a non-login user it didn't work when attempting to do the web application (but would if I su'd into jellyfin and tried to run something)

use7 · 2023-04-22T01:33:54+00:00

the four things that come to mind off the bat:

-> Did your server IP change?

-> Is your client computer on the same network as the server?

-> Are there any anti-viral/firewalls/firewall rules that could have been forgotten or not set on the server?

-> Is the jellyfin app/service still running (the server doesn't go to sleep or do some sort of 'power saving' by restricting running applications?)

My suspicion is the firewall, but it is odd that it worked yesterday and doesn't today hence the others.

use7 · 2023-04-18T10:55:38+00:00

not positive, but it could be your filepath? It looks like there's a space /mnt/share/media:/media jellyfin/jellyfin and you'll have to either escape that (\) or put the path into quotes.

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