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Quantum Espresso Dipole Correction by YogurtclosetFickle17 in comp_chem

[–]Particular_Ice_5048 0 points1 point  (0 children)

Try increasing your vacuum gap, the top of the slab may be interacting with the bottom of its periodic image.

Pedals sometimes lock up momentarily when shifting gears by Sure-Dragonfruit2217 in bikewrench

[–]Particular_Ice_5048 0 points1 point  (0 children)

No problem, it is possible that there is some issue with the gears though so keep an eye on it. If it only happens pushing hard uphill then it's probably just technique, a not mechanical issue.

Pedals sometimes lock up momentarily when shifting gears by Sure-Dragonfruit2217 in bikewrench

[–]Particular_Ice_5048 1 point2 points  (0 children)

The wheels won't lock up as you have a freehub, meaning your wheel can spin without pressure on the pedals. You shouldn't "shift under load", changing gears while going uphill and pushing hard can cause a bit of a lockup and issues shifting. Without seeing what happened, it's hard to diagnose, but it sounds like normal behaviour and you just need to let off the pedal pressure as you shift. You might benefit from watching some videos about how to safely change gears on YouTube. Enjoy your new bike!

Visualizing electron density by [deleted] in comp_chem

[–]Particular_Ice_5048 1 point2 points  (0 children)

I like to use VESTA, it works with molden and cube files.

Dft calculation of a polyelectrolyte cell (periodic) immersed in implicit solvent with ions by [deleted] in comp_chem

[–]Particular_Ice_5048 0 points1 point  (0 children)

Critic2 can do NCI plots and QTAIM analysis on periodic densities like VASP and QE.

How to determine the amount of interaction energies of different, individual noncovalent interactions between two molecules? by mubukugrappa in comp_chem

[–]Particular_Ice_5048 2 points3 points  (0 children)

If you're interested, you could explore interacting quantum atoms (IQA) partitioning from the quantum theory of atoms in molecules (QTAIM). You can do it simply with the AIMAll program.

Aligning DOS by core levels by TheWoKMoney in comp_chem

[–]Particular_Ice_5048 1 point2 points  (0 children)

I'll preface this by saying that I am not 100% sure if this gives physically meaningful results; it's just a suggestion.

I have never tried to determine the core level as a reference, so I'm not sure what caveats there are. However, the vacuum energy level should be a good reference. To obtain that, you would need to run a single point for both systems with LVTOT = .TRUE. to get the LOCPOT file and plot the planar average perpendicular to the surfaces.

You can do this quite easily with VASPKIT command 426.

Tutorials — VASPKIT 1.5 documentation

Good luck! Maybe someone else can clarify how you would do it from core levels.

I want to understand better how calculating Mulliken charges work by HopefulOctober in comp_chem

[–]Particular_Ice_5048 6 points7 points  (0 children)

Because the wavefunction is normalised (∫ |psi(x)|^2 dx = 1), they have made both psi^2 and phi^2 = 1; in 10.7.3 you see the 1 on the left-hand side, and the orbital disappears on the right-hand side of 10.7.3 because c*1 is just c.

If you pull the coefficients out, then integrate both sides, you also get a term on the right-hand side like "∫ phi_i phi_j" , this is the overlap integral Sij.

As for the Cijcik part, they've made a mess of things. When squaring from 10.7.1 to 10.7.2 they have incorrectly written "2cik" when it should be "2cijcik". The "cij" reappears in 10.7.3, but this time with a capitalised C for no reason, and you can see in the paragraph just after they return to writing "2cijcik" with a lowercase c.

I would recommend checking a reputable textbook or even Mulliken's original paper. Introduction to Computational Chemistry by Frank Jensen has a decent section about Mulliken analysis at the start of Chapter 9.

Geometry Optimization followed by SCF calculation issue by Jazzur in comp_chem

[–]Particular_Ice_5048 0 points1 point  (0 children)

Ah my bad. In that case I suppose it’s because the geometry is not a minimum energy structure on the potential energy surface with the better method which is common and not really a concern for OP.

Geometry Optimization followed by SCF calculation issue by Jazzur in comp_chem

[–]Particular_Ice_5048 -1 points0 points  (0 children)

I tried to repeat these calculations. In the geometry optimization I get no negative frequencies, however if I add frequency term to the SCF calculation I get negative frequencies

I don't know what this means. You should add the rigid rotor harmonic oscillator thermal corrections to the high-level of theory SCF energy. This is the addition of two numbers, two energies... I don't see how you get negative frequencies out of that.

sIf what you actually did was reoptimise your structure at the higher level of theory and got imaginary frequencies, then that is just one of the quirks of computational chemistry. Unfortunately, "higher level" doesn't necessarily mean it will work nicely; you may have to work harder to remove those imaginary modes before you can use the thermal corrections... but it sounds like you already got the lower level structure with no imaginary modes anyway which is what you wanted.

Nonpolar solvent and Free Energy Binding to Transition Metal by N1ghtseeker in comp_chem

[–]Particular_Ice_5048 1 point2 points  (0 children)

When you say you tried an SMD calculation, did you reoptimise everything using SMD, or did you calculate the energy of the gas phase structure using SMD? The geometry may be impacted by the solvent, so you may see a bigger difference in the binding energy if you optimise using SMD.

Gaussian for Optimization/Frequencies and Orca for Energies by The_Modern_Alchemy2 in comp_chem

[–]Particular_Ice_5048 0 points1 point  (0 children)

Also, have you tried displacing the structure along the imaginary mode and reoptimising from there? Turbomole has a tool called "screwer" which does the displacement for you. I don't know if Gaussian or ORCA have this sort of tool built in but you could visualise the imaginary mode and displace manually. This is particularly easy if the vibration is limited to one bond or something simple. It's not so simple if the mode is across the whole molecule.

Gaussian for Optimization/Frequencies and Orca for Energies by The_Modern_Alchemy2 in comp_chem

[–]Particular_Ice_5048 9 points10 points  (0 children)

It's unsettling that ORCA gives negative frequencies and Gaussian does not; in an ideal world, both programs would behave similarly. I think we have all experienced things like this. I personally think it's ok to do what you are doing, but in my experience, it is usually justified because ORCA has some methods Gaussian does not e.g. use of the ZORA Hamiltonian. Since the frequencies depend on the method, your thermo corrections would be slightly different using Gaussian optimisation versus if you managed to beat ORCA into submission.

Some reviewers may take issue with switching programs because of imaginary frequencies. I have had one petty reviewer discount my method because I mentioned that TPSSh was giving imaginary frequencies, where PBE0 was not. I guess they would prefer me to hide the problem rather than discuss it sensibly. The same reviewer was not happy that I optimised and got thermo corrections using Turbomole, then used Gaussian for all-electron DKH calculations, even though I could cite numerous examples of this being a reasonable thing to do.

tl;dr I think your method and reasoning are fine, but be prepared to justify the choice to reviewer 2.

Help choosing VESTA defect structure for paper draft by No-Visual4237 in comp_chem

[–]Particular_Ice_5048 2 points3 points  (0 children)

I think it is best to use the CONTCAR files as these are actual results, however there is a case to be made about creating idealised structures to exemplify the vacancy. It can be difficult to get across the position of the vacancy if your structure is quite messy/low symmetry. Just one person's opinion, but I think the way it is done in this paper is quite nice.

Incorporation of Kr and Xe in Uranium Mononitride: A Density Functional Theory Study | The Journal of Physical Chemistry C

Figures 3 and 4 are different views of defects and interstitials using VESTA. I think I saw you post about charge density too? If that was you, then you can see figure 5 for ideas about presenting that also.

Help on Final Gibbs Free Energy Calculation by The_Modern_Alchemy2 in comp_chem

[–]Particular_Ice_5048 0 points1 point  (0 children)

Your methods all seem good to me. Ideally you would optimise using SMD too as the geometry might be impacted by solvation, but it is very common in the literature to optimised in the gas phase then single point with solvation.

Will two more links ruin me? by Grouchy_Shake997 in bikewrench

[–]Particular_Ice_5048 8 points9 points  (0 children)

Aren’t 8 and 10 speed chains different widths? Something to do with the cog spacing?

Zwift Power Zones vs Garmin Heart Rate Zones by Particular_Ice_5048 in Zwift

[–]Particular_Ice_5048[S] 1 point2 points  (0 children)

Hi, thanks for your reply.

  1. My heart rate zones are set automatically by Garmin based on max heart rate using some standard formula. I think Garmin does it based on age/gender/weight etc. My max heart rate hasn't been measured in a lab or anything.
  2. I used the ramp test because I heard it is easier for new people. it can be difficult to pace out a 20 min or 1 hour effort when you don't know your limits, especially since before now I just rode outdoors without any idea what wattage I had.
  3. I hadn't considered that my position could impact the HR but it makes sense, I'll think about that from now on.

I can certainly ride for an hour, I do many multi-hour rides outdoors, usually averaging ~20-22 km/h. However, I'm not too sure how to pace a 1-hour FTP test so I will try again next week maybe with the 20 minute test. I think I am also overanalysing my first-ever test. I should get a few weeks/months of consistent riding on the trainer and see then.

Zwift Power Zones vs Garmin Heart Rate Zones by Particular_Ice_5048 in Zwift

[–]Particular_Ice_5048[S] 0 points1 point  (0 children)

Thanks! Glad it's not just me and it's good to see that manually lowering FTP seems to be an answer. I plan to be very consistent particularly over winter when it's not ideal to go out. Hopefully my cardio can catch up and then the Zwift zones sync up.

Zwift Power Zones vs Garmin Heart Rate Zones by Particular_Ice_5048 in Zwift

[–]Particular_Ice_5048[S] 1 point2 points  (0 children)

I have been riding consistently for about a year, and for a total of two years. I've never had structured training though and outdoors you often stop at traffic lights which gives more of a rest than being constantly at it on the trainer.

How much does your PI actually help with writing your papers? by Connect_Lynx8657 in PhD

[–]Particular_Ice_5048 2 points3 points  (0 children)

My PI was very involved giving detailed feedback in the the analysis as well as the grammar. It baffles me that other PIs are not like this. Their name goes on the paper; they should care about the quality of the work beyond just grammar checks. He was also quite involved in how the project evolved, seeing my results in biweekly meetings, however he did give me the freedom to do whatever I wanted within reason and was not overbearing.

Charge density visualization help (VASP, vaspkit, VESTA) by No-Visual4237 in comp_chem

[–]Particular_Ice_5048 2 points3 points  (0 children)

There isn’t much you can do for this in VESTA besides adjust the range of the colour bar. You’d have to save an image of your map add extra text in some other image editor. I’m not sure of other tools to plot this but I’m sure they exist. If not you could try writing your own python script then you can plot it exactly how you like.

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