Tyberius

general recent conversations

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HNQ for materials.stackexchange.com/?tab=hot

Tyberius

Mar 31 13:05

Bump to keep unfrozen

Modeling Matters!

Matters related to modeling matter, because modeling matters!

Tyberius

Mar 19 17:17

@user1271772 It looks like Sloshy might be down for all of StackExchange (though Stackoverflow chat is apparently okay). github.com/tripleee/sloshy/issues/116

Economics

For economic questions but also general discussion.

Tyberius

Nov 11, 2023 21:55

Would you like me to migrate it here or just close it?

Tyberius

Nov 11, 2023 21:55

@1muflon1 @EconJohn @KitsuneCavalry I think this question got posted on the wrong site: mattermodeling.stackexchange.com/questions/11891/…

Ask a Moderator

For any questions you might have for the Mat Mod Mods (Matter ...

Tyberius

Oct 12, 2023 19:56

From user's accounts, mods can see a more up to date time since the user last logged in. I vaguely remember there being a meta post awhile back about reducing the granularity/accuracy of daily activity that a typical user could see about another user.

Tyberius

Oct 12, 2023 16:03

@user1271772 I noticed the user had returned yesterday and thought they might reply. But I think closing it is probably the better way to give the user a "push" to reply.

Tyberius

Aug 11, 2023 18:51

chat.meta.stackexchange.com/rooms/1702/… This room has all the comments on Meta StackExchange.

Tyberius

Aug 11, 2023 18:50

@user1271772 Potentially worth looking into: https://github.com/SOBotics/Boson/blob/master/docs/commands.md

There is a bot that can auto track comments and port them to a chat room. I would have to see how fancy the filtering can be to make it send question/answer comments to the right room. Worst case, we could have a room that served as a repository of all comments and these could moved as needed to the appropriate room.

Tyberius

Jul 14, 2023 18:02

I'm definitely not a fan of ads, but any site is going to be looking for more ways to make money and these sorts of ads are a very common way of doing that.

I guess its more so that I've resigned myself in the short term ads being the main way sites get funding.

But I went back and read the meta post again and I do think its a jumping off point for a community discussion and/or negotiating with stackexchange, so I added the featured tag.

Tyberius

Jul 13, 2023 13:42

I think it will ultimately have the same result, but I think it makes a stronger case if the question is left "neutral" while answers advocate for different positions (though I assume it will wind up just being the "against" position as an answer; I doubt anyone is really strongly "for" having more ads).

Tyberius

Jul 13, 2023 13:40

@user1271772 I had held off on featuring it because I saw it more as stating the (assumed) community position on the issue to the company rather than seeking input on how the community felt about the issue.

I'm fairly ambivalent about the issue, so I didn't want featuring it to be seen as a "vote" one way or another.

I can feature it as is, but I think it would be better if the bulk of the post was in an answer and the question was rephrased to seek community opinion.

Tyberius

Jun 12, 2023 16:58

My understanding was this question was migrated from Chem SE just a few days ago (Jun 9th). The user doesn't have a profile on our site yet because they seemingly haven't visited since the migration.

Tyberius

Mar 4, 2023 01:52

@NikeDattani there was an earlier voter who voted to close as a dupe. It originally had a comment, but it seems that after I closed it as a dupe, the community user deleted the comment.

Tyberius

Feb 17, 2023 17:48

It seems their bounty got refunded. Usually that doesn't happen, but maybe there is an exception for when a question is deleted by the Community user bot. The fact this is somewhat of a weird edge case (their rep went up because a now deleted question had a long overdue bounty refunded) is probably why the reporting on it is confusing.

Tyberius

Feb 17, 2023 17:47

It had a bounty on it back in July of last year for 100 rep. It was closed a little over two weeks ago and then the Community user deleted it 6 days ago because it had no upvotes, no answers, was closed, and existed for more than a year (I think, may need to look up the roomba criteria again). The day it was deleted is the day they earned 100 rep and it was all from that deleted question.

Tyberius

Feb 17, 2023 17:45

Interestingly, it seems to be tied to the deletion of this question: mattermodeling.stackexchange.com/questions/9414/…

Tyberius

Feb 11, 2023 01:55

I don't mind changing it to "on hold". Might get flack from SE since they went through the process of getting rid of the on hold status a while back, but since it isn't functionally any different from "abandoned", I don't see any problem with it and they haven't voiced any concerns about the "abandoned" close reason.

Tyberius

Feb 11, 2023 01:52

Merge would still require making a tag for the correct spelling. Since it was just two questions (one of which was immediately closed as a duplicate), I figured it was easier to just copy the description over and change the tag on the two questions. The delay for the search to update would still apply.

Tyberius

Feb 11, 2023 01:49

I think it takes some time for the search to update and it will take a little while for crystalfb to disappear now that it's on no questions.

Tyberius

Feb 11, 2023 01:48

I was just about to copy it over. You basically can't edit a tag name (or at least it wasn't obvious to me how) so I just made a new tag and was going to port over the short description.

Tyberius

Feb 11, 2023 01:46

@NikeDattani I had vaguely remembered someone one in the comments saying it shouldn't be closed, but looking again didn't see anything even deleted comments. I was going to ask this other user why, but since I'm apparently just misremembering, I went ahead and closed it.

Tyberius

Feb 10, 2023 21:13

@NikeDattani Generally, we can't edit the help section. This page is the only one that I know is editable by mods.

Orca

Discussion related to the Orca electronic structure program

Tyberius

Oct 12, 2023 14:17

@wzkchem5 only valid for all auxiliary generation methods suggested so far... the alternative is to build an auxiliary basis by explicit optimization which is a wholly different thing — Susi Lehtola Oct 8 at 9:08

Tyberius

Oct 12, 2023 14:17

@SusiLehtola Thanks, that was a nice read! However I think this argument is only valid for specific automatic generation approaches. Suppose we have an algorithm that can, e.g. generate f auxiliary functions even for an sp basis set, instead of generating only up to twice the ang. mom. of the orbital basis set (i.e. up to d in this case). Then we can still get arbitrarily good accuracy if we add more and more aux. basis functions. Of course, one cannot generate the f functions by atom Cholesky decomposition, but one can at least generate them empirically. I wonder why no one has done so. — wzkchem5 Oct 7 at 8:19

Tyberius

Oct 12, 2023 14:17

@wzkchem5 yes, generate an auxiliary basis for a triple zeta basis for the same family. A double zeta basis may not have functions of a sufficiently high angular momentum, leading to large RI errors as the one-center approximation is not valid, see doi.org/10.1021/acs.jctc.1c00607 — Susi Lehtola Sep 28 at 16:47

Tyberius

Oct 12, 2023 14:17

@SusiLehtola By the way, what is your suggestion when one wants to use a double zeta basis set (say aug-cc-pVDZ-PP), but there is no dedicated auxiliary basis set for it? If using AutoAux is not an option due to accuracy concerns, do you recommend turning off RI, or use the dedicated auxiliary basis set of another double zeta basis set, or use AutoAux on a similar triple zeta basis set (e.g. aug-cc-pVTZ-PP)? — wzkchem5 Sep 27 at 15:48

Tyberius

Oct 12, 2023 14:17

@SusiLehtola Thanks for pointing this out. I checked the AutoAux paper (DOI: 10.1021/acs.jctc.6b01041), and it seems that for double zeta basis sets, AutoAux is usually more accurate than hand-tuned aux basis sets for total energies, but less accurate for reaction energies. In the most unfavorable case (MP2 reaction energies of the DC9 benchmark set, Table 5), the average error of AutoAux is 0.16 kcal/mol, while that of the hand-tuned basis sets (def2/JK + def2/C) is 0.06 kcal/mol. I'm not sure if this suffices to show that AutoAux is unsuitable for double zeta basis sets. — wzkchem5 Sep 27 at 15:45

Tyberius

Oct 12, 2023 14:17

@J.Doe Since you are only using 4/6 of your cores, please use one of the remaining two to check whether or not newGTO Br,Zn,I "aug-cc-pVDZ-PP" end works with multiple elements at once rather than asking here. If it doesn't work, and you want to know how to modify your input file to make it work, you can ask that in a separate post. I can add more guidance here if necessary. — Nike Dattani Sep 27 at 15:44

Tyberius

Oct 12, 2023 14:16

I have already launched a bash script that is looping over 70 input files and uses 4 out of 6 cores on my system. I didn't want to launch any separate jobs right now in case a lack of resources crashes the current loop. so I thought it would just be a simple, quick question for clarification — J.Doe Sep 27 at 15:17

Tyberius

Oct 12, 2023 14:16

@J.Doe The last sentence in your most recent comment looks like a new question that would preferably be asked in a separate post (not in this one) since it doesn't have anything to do with the title of this thread. Also, have you tried to see if your suggested line works with multiple elements at once? — Nike Dattani Sep 27 at 14:51

Tyberius

Oct 12, 2023 14:16

adding autoaux has done the trick, thanks a lot. I have found out though, that I have multiple atoms for which I should/need to use aug-cc-pVDZ-PP. I do a lot of calculations and some of the mols contain Bromine and Iodine. aug-cc-pVDZ is only defined for hydrogen-krypton. Can I just use newGTO Br,Zn,I "aug-cc-pVDZ-PP" end to specify a different basis set for multiple elements at once? — J.Doe Sep 27 at 14:35

Tyberius

Oct 12, 2023 14:16

"The auxiliary basis sets generated by AutoAux are essentially always suitable for the orbital basis set that you specified." This is not correct. Automatic auxiliary basis sets are only accurate if the orbital basis is at least of polarized triple-zeta quality. — Susi Lehtola Sep 27 at 13:49

Tyberius

Oct 12, 2023 14:15

A: ORCA crashes because of RI approximation?

What the doc wants to say is that the program may make an automatic choice of the auxiliary basis set (typically def2/J for non-relativistic calculations and SARC/J for relativistic ones, if I'm not mistaken), but in some (not all) cases they may not be suited for your basis set. It is well-estab...

Tyberius

Feb 5, 2023 14:03

room topic changed to Orca: Discussion related to the Orca electronic structure program [orca]

Milestones

mattermodeling.stackexchange.com

Tyberius

Sep 22, 2023 16:10

@user1271772 I'm at 1232 days visited. I have definitely been less active on the site this year.

The mathematics and science behind Ma…

mattermodeling.stackexchange.com

Tyberius

Aug 12, 2023 22:08

$G_{ads} = E_{oxidized} + F_{vib} - E_{clean} - N_O\left [\frac{1}{2}E_{O_2} + \Delta\mu_O(T,P^0) + \frac{2.303}{2}k_BTlog\left(\frac{P_{O_2}}{P_O}\right ) \right ]$. This is the equation I plotted. From literature, the authors talk about desorption at positive $G_{ads}$ — Nana Kofi Boakye yesterday

Tyberius

Aug 12, 2023 22:08

Equations can be typed in comments the same way that they can be done for posts, but the equation in my comment from 50 minutes ago does not appear correctly because I forgot two closing brackets! Here is the equation: $\Delta G = G_{\textrm{adsorbed}} - G_{\textrm{desorbed}}$. — Nike Dattani yesterday

Tyberius

Aug 12, 2023 22:08

Sorry for that I was only showing the link to the earlier post since I can't type the equation in a comment. So I have an oxidized surface. And I want to check the stability of the surface with variation in pressure and temperature as the link depicts. — Nana Kofi Boakye yesterday

Tyberius

Aug 12, 2023 22:08

Please try to use full sentences when you communicate to me. — Nike Dattani yesterday

Tyberius

Aug 12, 2023 22:07

mattermodeling.stackexchange.com/questions/11405/… — Nana Kofi Boakye yesterday

Tyberius

Aug 12, 2023 22:07

If what is plotted is $\Delta G = G_{\textrm{adsorbed} - G_{\textrm{desorbed}$, then a positive value would mean that the desorbed of the system has a lower free energy and is hence more stable. This would suggest to me that desoption would occur at low pressures and from 1100K to 1500K. From where did you get this figure? — Nike Dattani yesterday

Tyberius

Aug 12, 2023 22:07

Ok thanks Sir for the explanation. Does it mean when the free energy becomes positive as seen at low pressures and high temperatures (1100 - 1500 K) there will be desorption? — Nana Kofi Boakye yesterday

Tyberius

Aug 12, 2023 22:06

A: What is the meaning of a "free energy per unit surface area" vs "pressure" plot?

The graph does show that at high pressures the $\Delta G$ per surface area values are lower, which would usually indicate stability. I agree with you that as the pressure goes lower, the stability reduces. However I disagree regarding temperature: As the temperatures decrease (from the green curv...

Tyberius

Feb 5, 2023 13:55

@HemanthHaridas but like I already wrote above, if you have analytic gradients you only need one such displacement, see the second-to-last equation. — Susi Lehtola 4 hours ago

Tyberius

Feb 5, 2023 13:54

This is the point of confusion for me. Equations to compute second order partial derivatives always require two of such displacements applied together. However, as I mentioned in the question, the temporary files generated by ORCA doesn't seem to do that. — Hemanth Haridas 10 hours ago

Tyberius

Feb 5, 2023 13:54

No, $\hat{e}_i$ is the unit vector in the $i$th direction in the compound indexing. For instance, if one uses C-style indexing from 0 to 3N-1 as in the post and $i=1$ and $j=2$, then you are changing the y and z coordinates of the first atom. Note that you can also have the case $i=j$.. — Susi Lehtola 19 hours ago

GAUSSIAN

Questions about use of the Gaussian electronic structure program

Tyberius

Jul 21, 2023 17:09

Q: Cannot optimize hexa aqua Cu(II) and Fe(III)

I try to optimize very simple systems - hexa aqua Cu(II) and hexa aqua Fe(III) - in Gaussian 16. The inputs are provided in the end of the post. Unfortunately, the geometry optimization never finishes as the water molecules keeps oscillating around the metal center. What to do? Thanks Cu_II.inp #...

Downvoting

What is the purpose of down votes on the site

Tyberius

Apr 8, 2023 14:21

@user1271772 It had been closed by voters as needing detail and then the author deleted it.

Tyberius

Mar 31, 2023 23:39

Bump

SIESTA

For discussion about the SIESTA electronic structure program

Tyberius

Feb 11, 2023 12:20

@nickpapior We made this new chat room for discussing SIESTA and I made you a room owner, which gives you certain extra privileges, namely the ability to add feeds. @NikeDattani was hoping we could get the room set up with useful feeds for SIESTA users if you had any in mind.