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6:16 AM
do I see a @Dissenter here?
 
just a tschoppi here @Martin-マーチン
 
Well, well, well.....
Hi @tschoppi :) Nice to see you
 
Heyoo, same to you
Writing summaries
Listening to some music
Life could be better
Just a random haiku for procrastination reasons
 
6:34 AM
Hark, awesome
Listening to music/ compiling some source code/ life could be worse
Wow, the metric is not even close to right in this one
 
Haha, totally off there ^^
"compiling some source code" is always great. Go get a coffee
 
well, not quite... still reading intructions
i have the dull task of installing gamess, but i would like to do something more fancy
Also there is so much reading...
 
7:00 AM
compiling GAMESS is relatively simple
adopting rungms is tough
 
I know, but i am lazy O.o
nooooo
why would you say that
 
:D
i'm doing it currently
trust me
 
I don't even want to use that program
but i need to...
:'(
 
me too
 
I want to do fun little calculations...
not boring td-dft with sometimes ambiguous results...
I have not dug into that yet, but does gamess come with nto built in?
 
7:09 AM
As far as i know, no, GAMESS does not have NTO.
The linking of GAMESS to binary gamess.01.x was successful.
heh
Now it is benchmarking time!
:D
OpenMPI vs. IntelMPI
 
Haha, enjoy
I have no idea what you are talking about though ;)
 
My bet is on IntelMPI...
 
@Wildcat well... I don't see why i should use it then...
darn...
i don't like that project
 
0
Q: OpenMPI 1.4.3 vs. Intel MPI Efficiency question

AshmohanI noticed that the exact same code took 50% more time to run on OpenMPI than Intel. I use the following syntax to compile and run: Intel MPI Compiler: Redhat Fedora Core release 3 (Heidelberg), Kernel version: Linux 2.6.9-1.667smp x86_64 mpiicpc -o xxxx.cpp <filename> -lmpi OpenMPI 1.4.3: (C...

BTW I have no Idea what you people are talking about
 
That is exactly what I'm trying to check. People generally claim that Intel's MPI implementation is faster.
Let's check that on real-world calculations.
:D
 
7:17 AM
"real world" hahaha
 
@Martin-マーチン, btw, why do you need GAMESS? Why not something else?
 
I have g09 which i use most of the times
but for our collaboration i need gamess
 
I have exactly the same situation.
:D
 
There is apparently a routine in gamess that they need... I have no idea what they are talking about
and since i am talking only with the middle man, i don't even have a real clue what i am doing
for now, i am trying to get it running, while i am waiting for irc
btw @Wildcat how did your ecp experiment turn out?
 
not yet done with it
jobs are pending in queue :(
 
7:23 AM
while { compile GAMESS }; do { play games }; done
2
 
Is GAMESS that bad? I mean, I have no idea about all those programs, as I have yet to use one of them extensively...
 
GAMESS is definitely wrong name for a project
 
@Wildcat Ohhh... have not had this feeling in a long time... i am a one pc only guy
 
when you try to google something 99% of the time Google suggest "games" instead of "gamess"
XD
 
the name is bad, the documentation is for advanced people
the program itself should be fine
avogadro supports building input files and stuff...
so that's a plus
 
7:26 AM
@tschoppi, no, it is good. doesn't have all the staff commercial programs have and is slower, but overall a good program.
 
okay. well, thanks for your opinions
 
It's free, so it's a taker :D
 
there a lot of other free programs
NWChem, for instance
 
well, the cluster I have access to also provides turbomole and g09, precompiled and everything ^^
 
sure...
you will probably find most support for g09
and the doc is quite good actually
 
7:29 AM
@tschoppi, because they are usually faster & better supported
 
as long as you don't dive into iop
turbomole is awesome for dft and mp2
 
but turbomole input is the worst I've ever seen :D
 
and probably CC by now too
 
Molpro is the CC beast.
 
sorry for interruption, but there is very confusing question on main site.
0
A: Naming double bond sidechain

FreddyAccording to IUPAC rules first thing you need to see is longest carbon chain which is 10(deca) over here. Then while numbering the Carbon double bond is given preference. So above compound is 10 carbon chain in which 3rd carbon is double bonded. Thus, 3-methylenedecane is correct name. Few...

 
7:30 AM
@Wildcat It is for very advance users...
 
After reading LDC3 answer, I feel that is correct.
 
@Freddy someone should dive deep into the blue book
 
not me; I gotta go
 
I hope someone will.
 
I have no access to the book
 
7:34 AM
catch y'all later
 
bye @tschoppi
@Freddy Look at the question Loong linked as duplicate chemistry.stackexchange.com/q/28554/4945
 
But I think It should not be closed. It is very useful.
BTW need to go, lunch time
 
I think it is almost an exact duplicate
It's funny how they call the documentation on the homepage word processed... they did not even choose a font which is easier to use...
@GAMESS
 
 
1 hour later…
9:09 AM
So, IntelMPI is no faster than OpenMPI. :D
 
Well, well, well.... that was a very quick benchmark
 
 
1 hour later…
10:17 AM
Yes, but I already had OpenMPI numbers.
Besides, benchmark are supposed to be quick.
And dirty! :D
 
 
1 hour later…
11:24 AM
I feel tempted to downvote this because I'm jealous of what the SE designers have done for the Chemistry site. :( (I like our Mexican Hat though, but this is so chic!) — The Dark Side May 18 at 17:18
 
 
2 hours later…
1:32 PM
@Freddy Whats wrong with the Physics design?
 
 
2 hours later…
Max
3:48 PM
Is this meant to be a general chat for general questions?
 
@Max Most certainly.
 
Max
Oh, I see then. I have a quick question about sulfuric acid. I know it's a diprotic, but the titration curve only shows 1 "leap". Can this be explained somehow? It feels like I'm missing something obvious here
 
Which titration curve are you looking at? Perhaps your titration curve doesn't show the proper ranges to illustrate the second e.point.
 
Max
Well, in the book I'm reading it specifically says that it only has one leap, so I wasn't looking at any specific curve. I was just assuming that it was true
 
Sulfuric acid is a very strong acid, so even in pure water it quantitatively deprotonates to at least the bisulfate anion
 
3:55 PM
Oh okay so sulfuric acid readily dissociates to h+ plus HSO4- in solution.
 
Putting it loosely, its first leap happens at around pH -6
 
then you add base to deprotonate the second proton
what @NicolauSakerNeto said
 
Since you'll never do a titration experiment at a pH that low, you'll never see its first leap
All you see is the leap when the HSO4(-) <-> SO4(2-) buffer breaks
 
Max
Oh, how interesting! But I don't quite see how the first leap can happen at pH -6. I know it makes sense, but it's a bit different from how I usually think
 
Since we're talking loosely here, you know the Henderson-Hasselbach equation?
 
Max
3:59 PM
Hmm, don't think so. I'm not at a very high level yet
 
Ah well, nevermind that then
 
Max
Or I don't know any equation with that name. Let me google to see if I know it under a different name
 
Put simply, a buffer is at its best capacity when the pH of the solution is equal to the pKa of the acid you're adding
 
Max
Oh yeah, I think I know that one (I do, just looked it up!)
 
So, the first pKa of sulfuric acid is like -6
That means it would theoretically act as a buffer around that range
 
Max
4:02 PM
That makes sense. But is that the pKa for H2SO4 or HSO4-?
 
H2SO4
The pKa_1
 
Max
My mistake, you did say "sulfuric acid"
 
That means that, if you were to use sulfuric acid's first pKa as part of a buffer, it would only act as a buffer around say, pH -7 to -5
Actually to be honest now I think this is becoming less useful than I thought, playing too loose with the concept
So nevermind all that
 
Max
yeah, that makes sense. But if I start with the titration of H2SO4 with NaOH (or any strong base), what does the solution contain exactly?
is it H+ and HSO4-?
 
Yes
There is no actual H2SO4 molecules except in extremely concentrated solution
 
Max
4:07 PM
The problem for me is that I'm getting what you're saying (and I feel like I'm really close to getting a full grip of this), but practically thinking, I keep coming back to the conclusion that "most H2SO4 is neutralized already", which seems wrong
why isn't there another leap when H+ reacts with OH-?
shouldn't H+ react before the remaining HSO4- molecules?
 
Max
But that doesn't make a seperate leap?
 
Hmm, trying to think a bit
I'm not entirely sure, but this is part of why I stopped the explanation I was doing before
 
Max
It feels like it can be explained if somehow connected to the fact that the leap takes place around pH = -6
 
The further away from pH 7 you get, the smaller the leaps become
So that's why I went back on saying there would theoretically be a leap in pH at negative values for the H2SO4 molecule
 
Max
4:12 PM
But it confuses me, since I don't see any scenario when the pH would be negative
 
Well there's no reason pH can't be negative, it's not entirely uncommon, just not something useful for a titration experiment
 
Max
But is it possible during titration with H2SO4?
 
Possible yes, but no titration experiment ever is set up that way
At very high or very low pH values, you start getting deviations from linearity, which makes analytical calculations unnecessarily hard
 
Max
oh wait, I only need a higher concentration, right?
 
If you were to titrate sufficiently concentrated solution of H2SO4, then yes it would start off being a negative value, and then increase with the addition of NaOH
 
Max
4:15 PM
But if I exclude that, and actually have > 10^6 moles/litre, I would see the first leap?
 
I suppose so, however unphysical that may be
Though I have a feeling this is going in the wrong direction
A pH of -6 doesn't literally mean the solution contains 10^6 mol/L of H+
pH is properly defined as the antilogarithm of the activity of hydrogen ions in solution
It just so happens that for sufficiently dilute solutions, the activity is almost equal to the concentration, so that helps a lot
 
Max
Oh yeah, and that has to do with the incredibly large number, right?
 
You can get very high activities at not so high concentrations
 
Max
Haha, I never knew this
 
For example, a 10 mol/L solution of HCl will not have a pH of -1, but it could be -2 or -3
 
Max
4:21 PM
Is there a reason for that? (I guess it requires me to understand what you mean by activity)
 
Well, you may have noticed that often chemists put a disclaimer when talking about a reaction or a system, saying "in dilute aqueous solution..."
 
Max
Oh yeah
 
This is because when the solute has a very low concentration, the only types of interaction in the system are solute-solvent and solvent-solvent interactions
Solute molecules are too far apart on average to make a measurable amount of solute-solute interactions
This means that dilute solutions are easier to treat theoretically
In concentrated solutions, though, this doesn't work anymore
Now solute-solute interactions cannot be neglected
So this adds an additional layer of complication
Many of the equations obtained in dilute solution are now not valid, becoming only approximations
And the approximation gets worse as the solute gets more concentrated
 
Max
Oh wow. But that changes the entire definition of what pH is. So it's not -lg([H+]/(mol/dm^3))?
 
No, that was never the definition of pH
That's just an approximation in dilute solutions
 
Max
4:27 PM
so the [H+]-part is wrong, that is?
 
pH is defined based on activity, which is kind of like concentration, except multiplied by a factor called the activity coefficient
And this activity coefficient is imbued with all the non-idealities in the system
And yes, the [H+] part is wrong
 
Max
Oh, I see!
Chemistry is a lot different from what you first think, haha
 
25
A: What is the unit of pH?

PhilippThe real definition of the $\text{pH}$ is not in terms of concentration but in terms of the activity of a proton, \begin{equation} \text{pH} = - \log a_{\ce{H+}} \ , \end{equation} and the activity is a dimensionless quantity. You can think of the activity as a generalization of the mole frac...

It's fine, these are details that you learn about as you go
 
Max
I must say, thanks a lot! Both for the link and the detailed explanation
 
No problem, though I feel I could have done a lot better!
I'm not very good at explaining things to others yet
Sorry to use you as a test subject!
 
Max
4:30 PM
I wouldn't say you aren't. It made a lot of sense to me at least.
And trust me, there's a huge difference between this and what we're currently learning, haha
 
I imagine
Activity is usually reserved for second-year undergraduate chemistry students
But, the takehome
You never see the first leap a titration experiment for H2SO4 because the first proton is very acidic, and titration experiments don't venture far from pH 1-13
That's all you need to know
The rest was me rambling
You may also find this link interesting chemistry.stackexchange.com/q/5737/1499
There's quite a bit of depth to things, but you'll get to that in due time, if you so desire
 
@Wildcat I just deleted my comment
 
Max
4:47 PM
I was eating, but I get what you mean now! Thanks again!
 
Alright, glad to have done something for you
 
4:58 PM
Heh. Whenever I see questions related to old quantum theory, I feel myself like Morpheus. :D
A red pill or a blue pill?
You take the red pill—you stay in Wonderland, and I show you how deep the rabbit hole goes.
:)
This quantum rabbit hole goes so deep...
I'm not even sure someone ever reached its bottom...
I think I can safely say that nobody understands quantum mechanics. (c) Richard Feynman.
 
According to Richard Feynman, it is safe to say that no one understood quantum mechanics
Haha
 
@NicolauSakerNeto, yep. I was thinking about this quote also.
Though, I like Dirac approach to it. :D
 
What about it? The sea?
 
No, no. His general view of quantum theory. Let me find and quote it.
Here is the quote
[…] the main object of physical science is not the provision of pictures, but is the formulation of laws governing phenomena and the application of these laws to the discovery of new phenomena. If a picture exists, so much the better; but whether a picture exists or not is a matter of only secondary importance.
In the case of atomic phenomena no picture can be expected to exist in the usual sense of the word 'picture', by which is meant a model functioning essentially on classical lines. One may, however, extend the meaning of the word 'picture' to include any way of looking at the fundamental laws which makes their self-consistency obvious. With this extension, one may gradually acquire a picture of atomic phenomena by becoming familiar with the laws of the quantum theory.
From Dirac's Principles of Quantum Mechanics.
 
I see, that sounds pretty agreeable, if almost impossible
I don't mean to challenge his observation, getting used to quantum mechanics is just hard
Our poor little brains never evolved with such an application in mind
 
5:25 PM
And thus,
"Shut up and calculate!"
:D
While this slogan is sometimes attributed to Paul Dirac[64] or Richard Feynman, it seems to be due to David Mermin.[65]
 
Haha, I was going to mention that quote
Yes
I knew it was not from either of them
 
 
6 hours later…
11:16 PM
 
Command & Conquer go!
 

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