The Periodic Table

pentavalentcarbon

00:00

The thing it lacks is good (LaTeX-quality) math support, which you probably don't need.

DSVA

Yeah i will try that and also OneNote. I just noticed that I was using the shitty version included in windows rather than the pro version. The real version isn't that bad and seems to be able to do most of the stuff I want.

pentavalentcarbon

I also need to add properly-formatted code to my notes which is essentially impossible with Evernote. Again, not a problem that you have.

I've heard good things about OneNote, esp. on the Surface.

The drag-and-drop functionality in Evernote is really unmatched, especially with pulling stuff from the web.

So one of those is probably your best bet. But a non-free version of either, otherwise it'll piss you off.

Do you practice good file organization for your calculations/analysis?

DSVA

yeah but it's not possible to just copy/paste chemdraws into Evernote. Everything has disadvantages and advantages:-D

Yeah, everything pretty nice sorted into several layers of folders, works very well

pentavalentcarbon

Ok, good. People underestimate the importance of that, but it might not be obvious at first.

DSVA

yeah that and having a good naming scheme

pentavalentcarbon

00:05

Just like my experimental friends who do NMRs.

DSVA

Yeah, but there you use the connection to the lab notebook which makes it easy too:-D And I'm trained to do that I guess that's why I want to try to use one for computational work too

pentavalentcarbon

All the organic chemists I know have better organizational skills than the computational and theory people, because of their strict LN requirements.

So I know where you're coming from.

And you're right in that traditional ELNs are just bad for what we do.

This won't help you with a lab notebook, but something that can stay close to your calculations is a plain text file (README or README.md) that has more details about the calculations, if you don't feel like having 50+ character filenames or directories 10 levels deep.

(My notes tend to be in the style of that harmonic frequencies PDF, if you read it.)

DSVA

harmonic frequencies PDF ?

pentavalentcarbon

maybe it wasn't you, I thought it was you

dropbox.com/s/nz6nozp2yd96a82/post.pdf?dl=0

Someone on reddit asked how harmonic frequencies were calculated and trying to write math in those comment boxes is terrible.

gannex

00:25

does anyone know the name for the amine version of the aldol condensation?

can I call it like an aldamine condensation?

Jan

Wow … my brain … it took me three tries to realise that it’s not anime …

pentavalentcarbon

It'd be better if it was anime.

Jan

Are you reacting an enamine with an imine, an enamine with an aldehyde/ketone or an enolate with an imine?

gannex

OK I'm writing "anime condensation" just to check whether my TA actually reads this shit

Jan

The world would be better if it were anime. We would have catgirls =^,...,^=

gannex

00:28

No I'm reacting an amine with an aldehyde to form the carbinolamine

Jan

That’s not an aldol reaction?!?

gannex

whoops I'm forgetting my organic

it's just a regular condensation then I guess

DSVA

@pentavalentcarbon oh yes that's me. I just wasn't thinking about reddit. Thanks again for that

Jan

Amine + carbonyl is just ‘nucleophilic attack of nitrogen onto a carbonyl group.’

If you end up with an imine, it is a Schiff base formation.

gannex

ah ok it's just the Schiff base formation then

orthocresol

00:37

@Jan What would you call the enamine+imine reaction?

Jan

I don’t know.

orthocresol

:D

Jan

But enolate + imine is Mannich.

orthocresol

Ah, yeah, it is.

I basically call everything aldols.

Jan

Not sure about enamide + aldehyde either ^^'

orthocresol

00:38

"the nitrogen-aldol"

Jan

@orthocresol The Sonogashira-aldol … ;p

orthocresol

That sounds like a true anime reaction

2

gannex

crap I have to brush up on this stuff

orthocresol

To make it sound more Japanese, you have to transliterate "aldol": something like arudoru.

pentavalentcarbon

dangerous territory here

Jan

00:41

~~I’ve seen enough tentacles to know where this is going …~~

pentavalentcarbon

maybe...Absolute Territory

gannex

Zettai Ryoiki??

pentavalentcarbon

whether you like it or not, you're my friend now

Jan

Damnit, I missed the pun. Shame on me.

gannex

I think it is important to maintain the ideal ratio of 4:1:2.5 miniskirt:exposed thigh:socks

Jan

00:44

*stands in the corner ashamed of looking around the room*

pentavalentcarbon

Even if you only get the NGE reference you're still my friend.

I'm not informed enough to have an opinion on the ratio...yet.

gannex

honestly I watched NGE but I don't get the reference

I just dig Zettai Ryoiki

orthocresol

I'm lost. Should I be thankful?

pentavalentcarbon

yes, you should be

Jan

I didn’t watch NGE (it took me a while to figure it out) but … why would I attribute zettai ryoiki to NGE?

gannex

00:46

oh... is the term Zettai Ryoiki a reference to NGE?

Jan

No, you should be sad. You’re missing out on catgir… actually, be happy. Seals eat fish, cats eat fish so catgirls are competitors.

pentavalentcarbon

From TVTropes:

> the term being used as an homage to the AT fields in Neon Genesis Evangelion.

Jan

Aaaaaahaaaaa.

Learnt something new again.

(I’ll probably forget it, though.)

pentavalentcarbon

I guess "terror" can be translated as territory.

Jan

Which reminds me I’ve been wanting to buy a figurie all week …

pentavalentcarbon

00:48

> The idea of a "holy area no one can intrude upon" was where the current meaning of the term originated.

Oh, so that's how you can afford that stuff, you have to move up a pay grade from grad student to postdoc!

Jan

Actually, I bought my first figurines while I was still undergrad.

I started a habit of buying one at every con I visited (after visiting two or so without).

Melanie Shebel

Most popular unanswered question on the site:

2

Q: What factor determines the strength of reducing agents and oxidizing agents

The best reducing agents are located at the bottom left of the periodic table(low electronegativity) and the best oxidizing agents are located at the top right of the periodic table(high electronegativity),excluding noble gases. Is the factor that determines the strength of reducing agents and ox...

Jan

But then came a time when I was rea~lly broke and the tradition failed.

Melanie Shebel

(I ran a query.)

pentavalentcarbon

8777 times!

Now that number will go up some more.

Melanie Shebel

00:52

Yeah, so it's a good one for someone to answer. ;)

Melanie Shebel

01:04

I put the top ten in this meta post:

0

Q: Unanswered, open questions with high views

I modified a query to fit Chem.SE and to give us unanswered questions (that are open) that have a high number of views. You can also run the query for 1 or 2 answers if you want. I did find that there were some questions that were quite popular and disappointingly did not contain any answers. ...

discussion

1,3-feeds

1

Q: Unanswered, open questions with high views

I modified a query to fit Chem.SE and to give us unanswered questions (that are open) that have a high number of views. You can also run the query for one or two answers if you want. I did find that there were some questions that were quite popular and disappointingly did not contain any answers...

discussion

pentavalentcarbon

just realized I started working on a question for someone who hasn't accepted at least one other answer of mine that's rather detailed...this is a strong incentive to not do it

Melanie Shebel

You should still do it. Don't answer to get an accept, answer to get upvotes from other users who think your answer is awesome. And when someone comes in from the search engine and sees your answer and it HELPS them, they might register to the site and ask a question of their own.

Hey, @pentavalentcarbon, what does post cleaning queue on your profile mean?

pentavalentcarbon

something that I was supposed to edit but never got around to because I'm scatterbrained and distracted

I needed to do some research for that one, plus some pencil-and-paper stuff...I probably wanted to try answering it too but ehhh

anyway, I keep most of my SE notes and links in text files in my Dropbox, I don't know why I have that there

user228700

Hi everyone :-)

orthocresol

01:18

I dislike the people who don't accept too. Sometimes you poke them a bit, offer a bit of guidance, they will learn; sometimes they're gone the moment they get their answer.

That said, I feel like if you are answering a question, the asker is likely to come within the first demographic. @penta Especially if they're a repeat asker.

Melanie Shebel

Or they've asked a question and have abandoned the site. I'll be honest, I'm disheartened by it too.

user228700

Yesterday, another user told me that the direction of the dipole moment is from the positive center to the negative center of a bond, but that this has absolutely nothing to do with which atom is pulling the electrons in the bond (i.e. which atom is more electronegative)

pentavalentcarbon

This person is a repeat asker. There is someone else who has asked many questions, I answered several of them, all detailed IMO, and never accepted any of my answers. Or other users' answers. I no longer answer their questions, even though some would benefit me (maybe not others) greatly. It's irrational but true.

Melanie Shebel

@Kaumudi Did you ask this question on Chem.SE? I'm having a hard time finding your question.

user228700

@MelanieShebel No, no, I didn't :-)

Melanie Shebel

01:22

Sometimes I don't mark the answer right away because I need more time to hew or want to give others the opportunity to answer, but doing this repeatedly is sucky. :(\

user228700

Is this really true tho? He kept telling me how it is a coincidence that the arrow of the dipole moment is usually pointed at that atom doing the pulling.

Melanie Shebel

@Kaumudi Did you ask your question in this chat?

user228700

@MelanieShebel Yeah, I guess I did. Albeit, a different version of the same question.

user228700

I mean, I guess it makes a little sense, but what about this:

Melanie Shebel

I'm just asking so I can find the background information for this question.

If you ask your question on Chem.SE, you may get a more comprehensive answer. I'm just an undergrad. :S

user228700

01:24

user228700

@MelanieShebel Oh, that's OK. If I ask there, it might even get closed for being too homework-tsy or whatever.

Melanie Shebel

Not if you show your work/thoughts in the question.

user228700

Uhh, is it not OK to just ask here? I've sort of been stuck with this for like, 2 days now so I could really use some quick help .__.

Jan

@MelanieShebel One is off the list.

I thought, if it’s that popular I’ve got to rant against d-orbitals, haven’t I? ;)

Melanie Shebel

Haha!

user228700

01:31

Can anybody please help me to identify the direction of dipole moment of the individual bonds in that picture, please? _/\ _

Jan

Stop starring things that will make the catgirls fall out of focus! =Y____Y=

Melanie Shebel

Catgirls?

Jan

1 hour ago, by Jan

The world would be better if it were anime. We would have catgirls =^,...,^=

Melanie Shebel

Hahahaha

Loong

4 messages moved to Maid Café (メイド喫茶)

user228700

01:40

Anybody, please..? .__.

Jan

It’s really bad. Every time I type ripostatine, my fingers want to type ribostatine first.

pentavalentcarbon

5

Q: Why the direction of dipole moment is from negative charge to positive charge?

An electric dipole moment is defined as $p = q\times 2d$. How to understand it physically? Why the direction of the electric dipole moment is from negative charge to positive charge?

electrostatics conventions dipole-moment

Electric dipole moment

In physics, the electric dipole moment is a measure of the separation of positive and negative electrical charges within a system, that is, a measure of the system's overall polarity. The electric field strength of the dipole is proportional to the magnitude of dipole moment. The SI units for electric dipole moment are Coulomb-meter (C m), however the most commonly used unit is the Debye (D). Theoretically, an electric dipole is defined by the first-order term of the multipole expansion, and consists of two equal and opposite charges infinitely close together. This is unrealistic, as real dipoles...

By convention, the dipole moment points from the (partial) negative charge to the (partial) positive charge.

Can you clarify this statement?

> the direction of the dipole moment is from the positive center to the negative center of a bond

Jan

@pentavalentcarbon I think, there was a ‘chemistry definition’ somewhere …

pentavalentcarbon

urgggghhhhhhhhh

Loong

@pentavalentcarbon That's the old traditional definition in chemistry:

14

Q: What is the origin of the "positive-to-negative" convention concerning dipole moments in chemistry?

I'm a physics professor who often teaches students who have taken a lot of chemistry (read: pre-meds). In physics, the dipole moment of a charge configuration is defined as pointing from concentrations of negative charge towards concentrations of positive charge. This is embodied in the formul...

history-of-chemistry dipole

19

Q: Confusion about direction of dipole arrow in alpha-helices and other molecules

I understand that molecular dipoles are electric dipoles. And electric dipole moment vectors point from the negative to the positive charge. In class we learned to draw these special molecular dipole arrows (with a "plus" at the beginning) that point from the positive to the negative partial cha...

physical-chemistry dipole structural-biology

Jan

01:50

@Loong was ten seconds ahead of me.

pentavalentcarbon

> Both conventions seem to be derived from the bones of dead theories.

user228700

@pentavalentcarbon In Chemistry, however, isn't this convention the opposite?

Jan

Oh damn you chemobot.

pentavalentcarbon

I don't like touching this crap with a 10 foot pole.

ok, let me read a bit...

Loong

dx.doi.org/10.1351/goldbook.E01929

Jan

01:52

Yes, he can do !!!beer too.

pentavalentcarbon

Reading about certain non-physics topics in chemistry makes me want a !!beer.

Aha, we stalled @Chemobot.

Jan

And !!tea

Chemobot

pentavalentcarbon

Reading that first post and the answers is making my eyes bleed.

user228700

@pentavalentcarbon: I'm concerned with the statement that it is simply a coincidence that in a bond, the dipole moment points in the direction of the more electronegative atom.

Jan

01:55

@pentavalentcarbon I think he ignored your command, because mine came with deletion.

The good thing about @Kaumudi’s question is that it can be answered regardless of the direction of dipole moment.

pentavalentcarbon

Do you point along a bond as opposed to pointing somewhere in space, like the middle of the ring?

Yes, I agree about that.

Jan

By the way:

20

Q: How can the dipole moment of carbon monoxide be rationalised by molecular orbital theory?

Despite the fact that oxygen is much more electronegative than carbon, the bond in $\ce{CO}$ presents a weak dipole moment. This observation can easily be explained using the concept of "dative bond", that is, one bond is formed with two electrons from oxygen, producing a polarization $\ce{O\bond{->

bond theoretical-chemistry molecular-orbital-theory

user228700

@pentavalentcarbon I don't understand. What dyou mean?

Jan

The dipole moment of CO points opposite.

user228700

@Jan O.o

pentavalentcarbon

01:58

Where else would the dipole point? Nothing constrains it to be along bonds, unless you specifically want to talk about bond-oriented dipoles.

user228700

@pentavalentcarbon I am talking about dipole moments of individual bonds.

pentavalentcarbon

Btw, you don't need to ping me, I'll see it.

user228700

Force of habit, sorry.

pentavalentcarbon

Ok then. So that means if you consider a single bond, then of course the dipole vector has to lie along that bond in one direction or the other.

No worries.

So the question is about the dipole vector pointing to the more electronegative of the atoms, is it a coincidence or not...

user228700

Yes...

pentavalentcarbon

02:01

I would guess it isn't a coincidence?

user228700

OK, what about this molecule:

user228700

pentavalentcarbon

That's consistent, right?

Generally speaking?

Jan

Just to clarify again for somebody who hardly ever uses a direction of a dipole moment: which direction did you agree on?

pentavalentcarbon

We are agreeing on the chemist's convention, positive to negative.

user228700

02:03

Look at the carbon of the $COO^-Na^+$. Why is it that this carbon shows a positive inductive effect toward the carbon in the benzene ring?

Melanie Shebel

I do positive to negative, because I imagine the negative drawing the positive um... positiveness.

pentavalentcarbon

I see where you're going, and this will require an organic chemist for a better answer, but I think the point is that there's some through-ring inductive effect.

Loong

Sure, we could stop dictators and pandemics, but we could also make the signs on every damn diagram make sense.

user228700

Through-ring?

pentavalentcarbon

So, I remember from aromatic substitution that the nitro group will be much more electron withdrawing than almost anything else, including a carboxyl group.

Electrophilic aromatic directing groups

In organic chemistry, an electron donating group (EDG) or electron releasing group (ERG) is an atom or functional group that donates some of its electron density into a conjugated π system via resonance or inductive effects, thus making the π system more nucleophilic. When attached to a benzene molecule, an electron donating group makes it more likely to participate in electrophilic substitution reactions. Benzene itself will normally undergo substitutions by electrophiles, but additional substituents can alter the reaction rate or products by electronically or sterically affecting the interaction...

Jan

02:07

@pentavalentcarbon That is correct.

Melanie Shebel

<3 electrophilic aromatic directing group stuff.

Jan

As I tried to ask you and Kaumudi: which direction did you agree on for dipole moment?

pentavalentcarbon

I said "through ring" because you might be able to rationalize the electron withdrawing capability of the nitro group is so great that this effect on the electron density is felt all the way on the other side of the ring.

damn it Jan

Melanie Shebel

2 rep down, 198 to go for the day. I can do it, right?

Haha, jk.

pentavalentcarbon

5 mins ago, by pentavalentcarbon

We are agreeing on the chemist's convention, positive to negative.

Jan

02:08

Ooops >__<'

Ignore my idiocity.

I’ll use 3 a.m. as an excuse.

pentavalentcarbon

It's ok, the more you post about anime, the more I'll star. Easy deal.

user228700

Alright, so the nitro group pulls the electrons from the benzene ring, making that particular carbon positive and then that effect goes backward, until it reaches the carbon attached to the $COO^-Na^+$ and then the carbon in $COO^-Na^+$ is more negative than the carbon in the ring to which it is attached?

Jan

Well no.

user228700

Um, OK..?

Jan

A better depiction would have two arrows pointing outside from the ring. The carboxyl carbon is definitely much more positive than the ipso-carboxy carbon.

pentavalentcarbon

02:11

Ipso?

Jan

However, on a grand macroscopic scale of things, it is less positive than the nitro carbon so the dipole moment points towards the nitro group.

ipso = bonded to.

pentavalentcarbon

ok

I think we could debate about which direction that one dipole vector is pointing, though.

user228700

I don't understand this .__. (Mostly because of the complicated terminology that I am not used to just yet)

pentavalentcarbon

Yeah, complicated terminology, Jan!

What we're trying to say is that the "pull" from the nitro group is so strong that all the bond dipoles are pointing to that side.

user228700

Riight. And what if it was some other group whose inductive effect is not this strong?

Jan

02:14

But … if we consider dipole on a per-bond basis that is no longer the case.

pentavalentcarbon

It gets more complicated.

user228700

How?

pentavalentcarbon

Also true.

user228700

O.o I'm confused.

pentavalentcarbon

Well, here's the simplest case I can think of.

Consider the symmetric version of this, with a nitro group on both sides.

user228700

02:15

OK...

pentavalentcarbon

Where will the bond dipoles point?

user228700

Toward the nitro group?

Melanie Shebel

Anyone got any chemistry jokes I can add to my article? I've got some good ones, but I need to add more to make it awesome.

pentavalentcarbon

But there are two now!

@MelanieShebel no because all the good ones argon

Melanie Shebel

Bahaha

Yeah, that one's on there.

user228700

02:18

Like this, perhaps (?) :

user228700

pentavalentcarbon

Yes.

The point of that exercise was to show that the dipoles don't necessarily all have to point in the same general direction, like from one side of a molecule to the other.

user228700

Alright, so hang on, question. Is $COO^-Na^+$ a +I group?

Jan

No. -I

pentavalentcarbon

?

Jan

02:21

I should really, really, really go to bed.

pentavalentcarbon

Oh, I see it in the Wikipedia article. What's this notation mean?

user228700

OK, why? Won't the oxygen pull away some electrons from the carbon, making it positive?

Jan

But the -M effect is stronger.

user228700

^ This, BTW, is what I should've asked at the beginning.

pentavalentcarbon

What's +I? -M?

Jan

02:22

COONa in itself is an electron withdrawing group. Both inductively and mesomericly.

user228700

OK..?

Melanie Shebel

Yeah, and I should get a start on my physics homework. :S

Jan

I effects are inductive effects; electronegative groups or elements pull electrons away from other atoms: a -I effect.

Electropositive ones donate electrons: +I.

user228700

@Jan I though the the inductive effect doesn't depend on the group attached to the atom?

Jan

M (or others use R) effects are mesomeric (or resonance) effects. The same but not inductively but via resonance.

user228700

02:24

That it was always relative to hydrogen and not to the atom attached to it..?

user228700

@Jan Dammit, I misread this. Sorry.

Jan

If you replace a hydrogen atom with COONa, that COONa group will be more electron-withdrawing than hydrogen.

Also sorry @Melanie for going against my own standards. It is just so much more engrained to write oxidise even if there are oxidizes in the post ^^'

user228700

Okay. But the reason that the dipole moment points the other way is because of the mesomeric effect?

Melanie Shebel

No worries, I thought it was the OP. :P :P

Jan

In the drawing above, if you do a proper per-bond analysis, the dipole moment should point from the (positive) ring carbon to the (electron withdrawing) carboxy group.

However, you can only have one macroscopic dipole.

2

And the effect that NO2 exercises on the ring is stronger than the effect of the carboxylate.

user228700

02:28

@Jan THIS. O sweet lord, this is what I've been going on about.

pentavalentcarbon

+1 +1 +1

user228700

Alright, I understand. I should've come straight to you yesterday! .__.

user228700

Thanks thanks! :-)

Jan

Haha =D

And then also remember carbon monoxide: Sometimes the formally electropositive atom (carbon) is on the negative side of the dipole.

So it really is ‘coincidence’ that most dipole moments have the electronegative atom as being more negative.

Melanie Shebel

Just realized the argon joke is in my image for the article! Bahaha!

Jan

02:31

Now how can I up my otaku stats with Penta around?

pentavalentcarbon

do you have a MAL for me to judge harshly?

Melanie Shebel

otaku?

pentavalentcarbon

oh no, maybe we shouldn't do this...

Jan

No, but I have an anidb list.

pentavalentcarbon

Hmm, I've heard of it but know nothing about it. I'm still new and not as obsessed as many.

Jan

02:33

anidb.net/perl-bin/animedb.pl?show=mylist&uid=446194

user228700

@Jan Hmm, alright! (Although now I have to go and check why this is so in the case of $CO$ .__.)

hBy2Py

@pentavalentcarbon @Mel I keep a running list of run descriptions as comments at the top of my input files, and just number the input files sequentially. It bloats the files considerably, but I always have a full history of that series of computations by looking at the highest-numbered one.

Jan

@Kaumudi Unfortunately, it’s very non-trivial.

Melanie Shebel

@hBy2Py ?

Jan

AniDB is just basically a database site with good links to fansub groups and the ability to track what you’ve watched. And since I used it first … I never used anything else.

hBy2Py

02:35

@pentavalentcarbon OH. Sorry, @Mel

user228700

Damn :-/ I'll give it a try, anyway. They should really stop teaching this stuff in schools, tho. I learned in high school that the direction of the dipole moment is the same as the direction to the more electronegative atom's position in the bond.

Jan

Also I haven’t voted for a single thing yet. But I’ll start sometime soon™

@Kaumudi Well, that works in 99 % of the simple cases, so why not teach it?

user228700

In fact, that's how they went about defining dipole moment in Chemistry. Maybe my school just sucked big time :-/

pentavalentcarbon

A few things are telling me we have the same taste...

user228700

@Jan 99%, hmm. Still classified as acoincidence :-/

pentavalentcarbon

02:36

@hBy2Py I was talking about that to DSVA. You made an accidental ping.

hBy2Py

And crap, I just edited my prior chat message instead of writing a new one. <facepalm>

pentavalentcarbon

@Kaumudi As it turns out, for a crude approximation, it's not bad. Just another "high school acceptable" thing probably.

nice job Brain

also your presence has reminded me I promised you timings and I never delivered. Do you have the old ones still? I can check it now.

hBy2Py

I never did formal timings before v0.3.

One sec...

v0.3 benchmark data

pentavalentcarbon

> Compressions performed while all 8 cores fully occupied with ORCA computations.

ಠ_ಠ

hBy2Py

Before v0.3, I was doing a lot of the math element-by-element in the Python interpreter, instead of having numpy chug through it.

Hahaha.

Worst-case scenario, c'mon!

Would YOU have wanted to halt computation for a little snip of benchmarking?

pentavalentcarbon

02:42

True benchmarks have nothing else going on.

Otherwise you mess with the cache lines on the CPU and occupation of the floating point units.

Plus, if the disk is doing something, etc.

hBy2Py

Ok, ok, I'll redo the timings next time I have a break in my computations.

pentavalentcarbon

So the bottom two tables are probably ok, because you see the logical trend.

But the differences in the values in the top table are so small that the error from doing something else on the CPUs might be larger than the differences.

hBy2Py

<nod>

Jan

By the way: bedtime for me. Good night o/

pentavalentcarbon

o/

hBy2Py

02:45

Worst-case, doing thresholding and/or truncation doesn't cost much.

Night

pentavalentcarbon

Can you remind me how you measure the numerical error from thresholding/truncation?

Do you compare integrated values?

hBy2Py

I haven't yet, but I will at a later phase of the documentation.

pentavalentcarbon

Ah, ok. I couldn't remember if you were measuring error at all.

hBy2Py

Yeah, this data is purely a speed and compression factor check

Each data value is stored as its algebraic sign paired with its log10 value.

pentavalentcarbon

I only ask because we both only look at the things for visualization, but some people do stuff like "difference densities" between states and integrate the isosurfaces.

hBy2Py

02:48

Oh, absolutely -- it's crucial for QTAIM and stuff, too.

No, I'm playing with basin integrations and stuff -- those errors matter to me just as much as the isosurface quality.

The way h5py's "scale-offset" filter works, it chops off floating point values to the number of digits past the decimal you specify.

pentavalentcarbon

Ah. Ok, I know little to nothing about QTAIM, I'm just spouting off over here.

But good that you thought of it then.

hBy2Py

So, --trunc 3 would store three digits of the mantissa of each value.

I haven't put together a rigorous comparative panel of images, but on a quick check, isosurfaces don't really change much all the way down to -t 2.

pentavalentcarbon

Right, the images.

hBy2Py

Ah, integrating on the isosurfaces -- yeah, the lossiness really would matter there too, gotcha.

I'll note to add that to my list of things to check -- I had only been considering volumetric integrations.

pentavalentcarbon

Wait, I thought those were the same thing...am I wrong?

hBy2Py

02:53

Not sure

Do you mean, integrating inside the isosurfaces?

I'd read what you said as integrating on the surfaces... surface integrals of some sort.

pentavalentcarbon

Ohhh, I didn't mean that. I meant inside, like the voiume.

hBy2Py

Ahhk, yeah, same thing, then.

@pentavalentcarbon Chatted with Geoff Hutchinson a bit about h5cube and Avogadro -- turns out Avo2 has h5py support built in.

So, integrating support might be pretty easy.

pentavalentcarbon

He told me that they're working on an interface were you can add Python scripts so they appear in a menu and you can run them by just clicking on them, and they can do whatever you want.

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