The Periodic Table

Martin - マーチン

03:06

I have no idea what jonsca meant with self-actualisation...

graduated sites do not have self-evaluation any way..

so nothing to worry about

If you find bad posts, downvote, comment, flag ...

Martin - マーチン

06:43

Chemistry Dubstep

►

PH13

07:28

hi all

@Martin-マーチン how do you plot your nice orbital pictures?

e.g. in the SO3 thread

Martin - マーチン

@PH13 this would be gOpenMol which is a horribly outdated program, but I have a couple of scripts, that make it work just fabulously

I have not found any other program that is scriptable this nicely

inɒzɘmɒЯ.A.M

Hullo guys!

What's shaking?

Martin - マーチン

shaking what?

inɒzɘmɒЯ.A.M

A building.

A lab.

A test tube.

I dunno.

santiago

my left arm

inɒzɘmɒЯ.A.M

07:41

o/

santiago

i'll use my right arm

inɒzɘmɒЯ.A.M

\o

santiago

personal medical question chemistry.stackexchange.com/questions/33914/…

inɒzɘmɒЯ.A.M

@santiago My man this question is very nicely formatted!

santiago

lol

inɒzɘmɒЯ.A.M

07:45

They have invented a new method of paragraphing.

PH13

@Martin-マーチン Thanks ... I'll have a look at it

do you think it is appropriate to generate a question regarding the different softwares that are available out there? I think it's broad and it's more something like a review than a simple question

inɒzɘmɒЯ.A.M

@PH13 We had something in meta that asked if we should have a canonical question about software.

IIRC, the consensus was meh.

PH13

@Martin-マーチン meta.chemistry.stackexchange.com/questions/73/… this?

inɒzɘmɒЯ.A.M

No, this:

2

Q: Should we have a canonical software question?

We seem to get many questions like Chemical software for solving reactions and Application or website for chemical reaction emulation which ask for software that can "solve" chemical reactions. And we have a few other posts on various other types of software. It may be beneficial to create a si...

discussion

Wait there are no comments there?

@Martin we should decide about it. . .

Martin - マーチン

Meeehhhh

PH13

07:50

Well, I wasn't thinking of raction solvers but more of the various quantum chemical software packages that all can do certain things and it's hard to have a good overview on all of them. I think I know a lot of them but I'd like to share my knowledge and want to gain new insights into programs that I didn't found so far

inɒzɘmɒЯ.A.M

@Martin I'm thinking of writing a meta post asking for people about whether we should have canonical questions.

They're a good way to deal with octuplicates.

Martin - マーチン

not so sure about that

but go ahead write some meta

inɒzɘmɒЯ.A.M

@Martin-マーチン Other SEs are doin' it, it's so effective as long as it's only 1-5 questions.

Martin - マーチン

a big list would be not so great, since this is awfully hard to maintain

inɒzɘmɒЯ.A.M

Not as long as there are a few big lists.

@Martin we could even try having them on meta.

Martin - マーチン

07:55

Bring it to the table, i don't like big lists...

inɒzɘmɒЯ.A.M

ELL has a big list of references and they've decided it's better in their meta.

Martin - マーチン

hard to maintain, never complete

inɒzɘmɒЯ.A.M

That's how CWs are.

But no, it's not as hard to contain that you think.

Martin - マーチン

yeah, I don't like the whole idea of cw

inɒzɘmɒЯ.A.M

Let's fight

Martin - マーチン

07:56

meh.

inɒzɘmɒЯ.A.M

Meh.

Meeeeh.

PH13

also ... please enlighten me what OP and cw means ...

Martin - マーチン

@PH13 If you make your question specific enough, then there should not be a problem...

i have once asked a question, which got mixed votes about some software...

hang on, i'll look it up

inɒzɘmɒЯ.A.M

@PH13 OP sometimes means Original post and sometimes Original poster.

CW means community-wiki.

You can make your answer Community-wiki.

Martin - マーチン

@PH13 chemistry.stackexchange.com/q/9957/4945

@inɒzɘmɒЯ.A.M But you should not

inɒzɘmɒЯ.A.M

07:59

That way, the votes won't affect your rep.

@Martin-マーチン Yeah, unless it's terribly wrong.

Martin - マーチン

There are very few exceptions, where cw is okay, but most of the time it is not

inɒzɘmɒЯ.A.M

Yep.

PH13

My question would be like ... What quantum chemical postprocessing software do you use to generate journal appropriate images and why do you use it? Following by a list of programs that I know containing the informations on them that I have

that's very broad but also very special as it does not concern the whole chemistry but only the computational section

inɒzɘmɒЯ.A.M

If it becomes a shop recommendation thingy, it's unacceptable.

Martin - マーチン

Well the computation section should not be a problem.

Make the post more specific, tell us what you currently use, why you do not like it, and what you have tried else

But in general, I think this post would be very helpful

PH13

08:04

that's what I think, too

inɒzɘmɒЯ.A.M

Yes, I would upcoat it.

PH13

I'll think of an appropriate question

Martin - マーチン

@PH13 I'll certainly have a look on that... make it as objective as possible

I would really love to have Geoff answer this, and tell me more about avrogado...

i am so confused by the gui...

inɒzɘmɒЯ.A.M

Me too.

Martin - マーチン

and the lack of tutorial makes me sad

PH13

08:06

always, yeah

have you heard of multiwfn?

I like it very much ... but the graphics are odd

the main purpose of it right now is to convert f*cking molden-files to cube-file for nice orbitals in gaussview

Martin - マーチン

no, i don't know it, what does it do?

PH13

it does so much ... 400 pages function background + tutorial on nearly every function

multiwfn.codeplex.com ... for free

Martin - マーチン

@PH13 Y u no use cubegen????

PH13

cubegen can read molden files?

Martin - マーチン

dunno... but if you use gaussian... you should have checkpoint files...

PH13

08:09

I use ORCA, Turbomole, Gaussian, ... whatever I can. But they are all not very compatible among each other

but I like the visualisation of gaussview and therefor I need to create cube-files from other programs outputs

also molcas

Martin - マーチン

Okay... get it...

i hate gausview

i use chemcraft on my windows platform

and i use molden for checking most things

PH13

molden is super ugly xD

but if there is nothing else, I use it too

and for me chemcraft has an "unnatural" color code for atoms which is confusing

inɒzɘmɒЯ.A.M

K I GTG.

Cya guys!

PH13

cya

Martin - マーチン

bye

PH13

08:16

then there is Gabedit which is very potent in reading outputs and generating inputs but fails an easy to use orbital/general surface producting system. there is always a 100 click porcedure to get to new orbitals ... that's bad for comparing as you forgot what has been when the next one is created

Martin - マーチン

in chemcraft you can edit the colour schemes

i like it because of a couple of features i did not find in any other package so far...

And i love molden for it's genuine simplicity

it is fast

and it has a very nice z-mat editor

i am very used to that program

PH13

but those visualisations are always a punch in your face

Martin - マーチン

not necessarily

you can adjust a lot of things too

PH13

then tell me what I do wrong g

... how to make asterisks ... oô

Martin - マーチン

i thing you can now even produce high quality povray stuff

\*

PH13

08:20

*test*

thanks

Martin - マーチン

well... i do my visualisations now with chemcraft

because it is easier to use...

it has this wysiwyg stuff going for itself

when i am checking stuff i like molden, because it runs fast enough via x-win

i don't need to emulate anything

PH13

I will take a look at it

Martin - マーチン

I grew up with molden 3. something... and there are hugh improvements now implemented

but best of all... for simple stuff, it has a force field module, which allows you to preoptimise structures on the go

avogadro has something similar too iirc

...hang on... brb.

PH13

I like Avogadro for simple preoptimized input. But it crashed here very often what keeps me looking for other softwares that can do things better.

Martin - マーチン

i am back...

have you tried contacting Goeff about the crashes?

PH13

08:36

nope, there is no good contacting here ... but as the latest release is from 2013 I didn't think that there is still development

Martin - マーチン

They are currently building the next release, i think that is the reason why they stopped developing the older ones

PH13

the next release of Avogadro 1 or 2?

Avogadro 2 was something they should have kept a little longer "in lab" ^^

Martin - マーチン

they are building avogadro two i think

PH13

ok

Martin - マーチン

we have to wait and see... I think Goeff said something about next year...

PH13

08:45

ok

maybe they already know about all the crashes

Martin - マーチン

I don't know

i thought a2 was still experimental

PH13

it must be

Martin - マーチン

The last thing I remember hearing from A2 is, that it is still far from feature complete...

but Geoff always points out, that you can contact him about it directly

i mean via sourceforge: sourceforge.net/p/avogadro/bugs

PH13

great, then I think about using it

Martin - マーチン

09:07

If you have questions about the usage of avogadro, then you will certainly find help here...

PH13

not about using but about avoiding bugs ;D

Martin - マーチン

there are a couple of users on the site and with the more complicated stuff, the developer is also around...

PH13

do you follow some blogs related to comp chem?

Martin - マーチン

@PH13 A bug is a feature in disguise

PH13

xD

Martin - マーチン

09:09

not really... i am too lazy to read this stuff ;)

PH13

ok, I'm always searching for new ones

and I need one blogger with big impact to blog about some failure of at least g09 rev. a.02

Martin - マーチン

Why would you want that?

PH13

that peoples out there know about this failure and how to avoid it?

do you think that everyone should figure out this error by themselves?

Martin - マーチン

Nope, but are there really many people still using this?

Is the bug prevalent to later versions?

PH13

I only have access to this version so I have no chance to compare it

as it is an error withing computing the grimme-dispersion corrections only version past this implementation have to be considered

Martin - マーチン

09:20

okay... what kind of error is it?

PH13

we will update our version within the next 2 yrs as we think that there must be the next bigger update to g15 or whatsoever

you can include dispersion by using the iop(3/124=...) statement ... e.g. iop(3/124=30) equals the D3 and =40 the D3BJ correction

(according to gaussian.com/g_tech/g_iops/iops2.pdf)

now you can either opt and freq successively or by combining them to be optfreq

when you optfreq with iop(3/124=...) then the frequency calculation will not include the iop-statement

and as frequency calculations are something that takes quite much time it would be good to know about this issue

Martin - マーチン

Yeah that is right... I never run optfreq

You are in Jena right?

Do I recall that correctly?

PH13

I am

Martin - マーチン

Don't you have access to the HPC there?

PH13

I have

if you mean the cluster at the rechenzentrum

Martin - マーチン

09:32

Omega

uni-jena.de/Universit%C3%A4t/Einrichtungen/URZ/Dienste/…

PH13

exactly

G03 D.01 and G09 A.02

Martin - マーチン

so you should have access to rev d.01

PH13

that's G03

Martin - マーチン

arrrghhhh

my mistake

PH13

np

Martin - マーチン

09:33

well, well, well...

I'd use g03 then

less buggy

PH13

^^

Martin - マーチン

I would not expect a major revision this year or next year...

maybe in 2017

But you have the awesome version of turbomole

PH13

yeah .. we will wait for it as it has to contain a lot

Martin - マーチン

well then you'll buy the buggy version again

PH13

sure xD

maybe we have to wait even longer then

Martin - マーチン

09:36

I'd wait until rev B is out, which will not be before 2018

maybe 2019

PH13

indeed

this software is so overprized for what they deliver

but it's easy to use

Martin - マーチン

7k/site license

Isn't turbomole much more expensive?

PH13

not if you have friends, i guess

but I don't have that much information on the buying process

Martin - マーチン

hmmm... when I was in Marburg, there was always enough money for the latest version

it was a principle necessity

PH13

yeah .. it should. but somehow they don't want it

Martin - マーチン

09:45

Hmmm

did you have any course with Leticia Gonzalez?

PH13

no, I was one or two years to late for her

Martin - マーチン

:D She gives great talks...

well, there are a lot who can do that

and more who cannot

muharrharr

PH13

^^

the comp chem courses have now maybe half the size ... don't know ... but it was a big cut when she left

Martin - マーチン

I understand that, she is a big shot

i guess a lot left with her and she took a whole lot more ;)

like grants and stuff

PH13

maybe ... I have no idea about such things. but if you read what's written on her site she must have a lot stuff

Martin - マーチン

09:53

^^

I met her... she has a lot of stuff

you need a lot of stuff for the things she does

PH13

here it is usually gaussian for regular stuff, turbomole for fast dft stuff and molcas for the big things

Martin - マーチン

didn't turbomole heavily improve their cc and mp2 routines?

They still have no real means to find transition states and do irc, but for all ground state this should be good to go...

PH13

you sure know more than me as I am just starting to get into everything a little bit more

Martin - マーチン

You'll learn... probably fast ;)

But have a detailed look at the features of turbomole...

i really miss that program

PH13

they produce nice output. but the input is not so nice ;D

but I will have to look at it anyway

Martin - マーチン

10:10

I loved define... makes you feel like an advance computational chemist ;)

PH13

sorry that I'm a little absent .. I track cells

user4215

10:31

hi

PH13

hi

Martin - マーチン

@user4215 Hello

user4215

What books should I read to master Mcat chemistry from nothing?

Martin - マーチン

what is Mcat chemistry?

user4215

MCAT

PH13

10:33

the question still holds

Martin - マーチン

yes

PH13

@Martin-マーチン HALP ... chemistry.stackexchange.com/questions/33916/… ... that's such a useless point

Martin - マーチン

i have a look

hahahahahahahaah

:D

great entertainment

PH13

that's so hard ...

Martin - マーチン

how do you respond to that???

PH13

10:43

maybe "then you'd better learn for the next exam" would be appropriate

Martin - マーチン

Invent the periodic table...

PH13

xD

Martin - マーチン

10:56

@PH13 ... I have to go now... have a lot of fun, I am looking forward to reading the question about visualisation :D

PH13

let's see what I can produce ... I am no good questioner ^^

bye

bon

11:14

0

Q: Where to look for mineralites?

How would one determine the most likely place to locate sapphires in Victoria, Australia. What would be the most practical way to retrieve one without machinery?

inorganic-chemistry

0

Q: How is persian blue rock salt made?

How is persian blue rock salt made and what does it contain that makes it look blue ?

inorganic-chemistry

Does anyone want to weigh in on the comments here. I don't feel I'm getting anywhere.

PH13

Joel is great

bon

'I don't do chat rooms' - It gets better and better

PH13

it's like his comments on chemistry.stackexchange.com/questions/33916/…

bon

yeah I'm following all of them

PH13

I could use all my 10 flags on him oô

Todd Minehardt

13:02

do i bother responding to this guy Joel to placate him?

bon

No. I already tried.

PH13

I don't know if this is possible. But actually this conversations with him should not take place in the comments, right?

bon

I flagged the questions for migration and the comments for deletion so we just wait for the mods to deal with it.

I asked him to come to the chat room but he refused

PH13

I know

Todd Minehardt

ah, that's good - he's pretty rude...saw the chat room decline

i was going to suggest he go to a jewelry store in Victoria to find sapphire

PH13

13:05

that would be a great answer

upvote

Todd Minehardt

let me answer that now...

bon

I would leave it as a comment not an answer

PH13

indeed ... that was a joke ;)

Todd Minehardt

well, i can move it

done

let's see what he says :)

are you both across the pond from me (i'm in austin, texas)?

PH13

indeed

over here is part of the old world

Todd Minehardt

13:11

nice to meet you -

that's where all the good chemistry comes from :)

PH13

the nobel prices say something different most times ;D

nice to meet you too

PH13

13:30

I'm a little afk

hi and bye @Wildcat

Wildcat

@PH13, =O.O=

Hi everyone!

bon

hello

Todd Minehardt

hi

check out the Persian blue salt thread - a swing and a miss

Martin - マーチン

13:51

hi @ll

Todd Minehardt

hi martin

Martin - マーチン

@bon please check your flag history ;)

what else is up?

Anyone know what persian salt is?

Todd Minehardt

yes, just posted answer

Martin - マーチン

OMG!!!! OMG!!! @LordStryker

Wildcat

Hi @Martin-マーチン.

Martin - マーチン

13:54

o/

Wildcat

I have no idea what the heck persian salt is.

:D

Todd Minehardt

it's basically salt from Persia (Iran) :)

and it's blue

somebody posted an answer about Prussian blue

the whole thing is hysterical IMO

Martin - マーチン

:D

Todd Minehardt

this is one of those "let me Google that for you" deals

Martin - マーチン

Well sorry, but i have to go... see y'all later ...

Todd Minehardt

13:57

cheers

Transcript for