« first day (1174 days earlier)      last day (3510 days later) » 

00:06
Oh. . .I thought you meant crashing. . . Anyways, I gotta sleep.
good night @inɒzɘmɒЯ.A.M
 
2 hours later…
01:55
hi :)
Heyo!
Sorry, was reading the chat history
Poor bacteria.
^^
I don't know if they still live
Well, nice thing about 'em, is there's almost always more where those came from.
So, yeah, just about everything I've tried ORCA's Molden files with has not liked them: VMD, CASINO (quantum Monte Carlo: vallico.net/casinoqmc).
it seems as they were hard to cultivate ... so I would not be too sure about it g
at home I use ORCA and in office the molden files come either from Molcas or from Turbomoles tm2molden
MultiWFN likes them okay, but only because they wrote a special filter for them
01:59
xD
know your enemy
hehe
VMD claims to support Molden files -- it may or may not be happy with those from Molcas / Turbomole -- only way is to try
But it opens a lot of other formats, too, so I'd try everything those packages are able to export to
I'm in process of expanding my answer on OP, with an actual step-by-step for ORCA .plt files
just as you posted this answer I looked if VMD was still installed and it was ... but the renderer doesn't work ... so I stopped this project again very fast
that's great
Ugh - OpenGL problems?
nope, more the vmd-windows-connection thing ... I guess
there is this line with "explorer %s" which he doesn't like that much
That reminds me - Gerald Knizia's group has made another viewer, iboview (iboview.org), that uses some fancy OpenGL stuff that my OEM video card doesn't like very much
weird
02:02
Iboview is my newest tool ... so fancy
that's how I made my profile picture
METALLIC ORBITALLLLLSSSS
one of the most awesome programs ever
I was sad - I was looking forward to having tool at hand that's implemented the Knizia intrinsic orbitals
but I still have to figure out the other abilities of iboview ... not just the fancy orbitals
and what I don't really like about it is that it does not support every basis set
Eek, that is not so good.
Because of basis functions with too-high angular momentum or something?
02:07
pople basis sets are bad
def2 are good
I don't remember the reason ... I will have a look
Neese is HUGE on the Ahlrichs def2's. Considers their polarization coverage to be much more balanced, I think it is.
Can't be high angular momentum, then, if Pople sets are bad -- if anything, they're under-polarized / under-high-momentummed.
ok ... the error is about something else ... "Sorry, this program does not support Cartesian basis functions. Please use a spherical harmonic basis (e.g. def2-* or cc-pVnZ bases)"
Ahh, <nod>, that makes sense. Implementation is completely different for both of those
I thought ORCA's bases were laid out in Cartesian, though... maybe that's part of the problem? I'd have to check to be sure.
no, I can do it with whatever molden file I have
but I mean ... they all come either from orca, turbomole or molcas ^^
Ah, nope, ORCA's default is spherical harmonics
Manual p283
Are you seeing the 'does not support Cartesian' error if you use Pople bases in ORCA?
(ORCA/Pople --> Molden --> iboView)?
02:15
I have to try it. But maybe then there is also a Linux -> Windows problem?
Oh, very possibly
make sure you run 'unix2dos' on all files before transferring to Windows
in my molden->avogadro problem nothing changes with changing linebreaks
<nod>, but it depends on the software
not directly ... but maybe the error is somewhere between the lines
for example, if I work up an ORCA input file on Windows, copy to my Linux server, then try to run w/o 'dos2unix'ing it, ORCA chokes badly
02:16
I run "unix2dos" manually through notepad++ ... does it depend "where" I convert them?
that's true
dunno, I've only ever done it on the Linux side
ok
It is (or should be) an unambiguous transformation... but who knows.
^^
Avogadro has also another funny thing ... I drop my first molden file in it, then there are all thos atoms missing. When I throw in another molden file it crashes ^^
<nod>
02:18
I really want to use it, but it fights back as much as it can
All respect to Geoff & team for putting something together as ambitious as Avogadro, but it definitely has some stability issues
also when I want to use this pH stuff ... I don't really know how to use it, but pressing the buttons makes it crash
sure ... it has great potential
I would guess that might only work on things like proteins
yeah, maybe you're right
maybe Geoff knows more when he answers my e-mail
I really have made a lot of use of the SMILES fragment input.
Find what I want on Wik, copy the SMILES, dump it in, and boom: the molecule I want.
02:22
as you mention it ... the conformational search also fails for bigger molecules and makes everything crash :D
I've even magicked up some other stuff just out of my own head. SMILES is pretty helpful
hehehe, well, that might just be a 'bigness' problem. :-)
Am curious -- whence 'PH13'? You feel alkaline most of the time
?
it does a good job until somewhat around 80-90% and that it's enough
I used SMILES only fr conformational searches with RDKit
no ... I couldn't think of a better name ... and my usual name could be found to easy throughout the web so I needed something new to be at least some sort of anonymous }:->
I debated anonymity, then decided against it. Does mean I probably won't post much on Academia.SE or Workplace.SE, but I'm okay with that.
I have always big concerns about what I say and I don't like to be wrong. So I don't give my name that easy away that it doesn't make me feel awkward too fast and too easy.
it's awkward enough to be wrong ... xD
then not the whole internet has to know about who was wrong in detail
:-)
I've decided it's better for my ego to have my being-wrongs plain to see
02:29
that's great :)
Ok, gotta get this VMD step-by-step finished, then get to bed. Good luck wrestling your visualizations!
do this :)
thanks ^^
and good night
<tips hat>
g'night!
 
5 hours later…
08:00
o/ @Brian!
Welcome to our humble Periodic Table.
 
2 hours later…
09:59
heyho
 
1 hour later…
11:24
@Brian I got some orbitals out of a cube file with VMD now :)
but with molden files there seems to be a longer way to go, because there are - as you mentioned it before - several misunderstandings between the programming groups that let their programs write molden files
 
2 hours later…
13:16
@Martin-マーチン HALP
13:28
Can anyone recommend good books for Group Theory ?
poor people that have to write good books about this theme
0
Q: Visualization tag has reappeared - should we burninate it?

bonvisualization reappeared today. It was previously deleted after this meta discussion. Should we remove it again, or perhaps merge it with software?

BURNINATE THE COUNTRYSIDE
seems like I'm the devil
Anyway, @PH13 i've found this list prntscr.com/7skczw/direct in some lecture notes but I don't want to read all of those so I was wondering if there was one in particular that you could recommend
13:33
I cannot recommend you something on this field as I don't know enough about this stuff to give advice
14:01
@Hippalectryon @Hippalectryon I actually gained the best understanding of group theory as pertains to chemistry from the section on it in Wilson, Decius & Cross
@Brian thanks !
@Hippalectryon For more detailed applications, though, I would recommend either Harris & Bertolucci or Bishop. I haven't had to apply group theory too much, though, so YMMV.
I'm just willing to read it to have an insight of what it brings, I don't need too specific applications :D I just do it because why not
Mmk -- yeah, I'd do WD&C for understanding of the symmetry operations and groups themselves, and Harris & Bertolucci for insight into how group theory is useful.
 
1 hour later…
15:26
Guys, @PH13, SOMEONE!
hm?
Make me forget my thirst.
Are you tracking bacteria @PH13?
shouldn't you be trained?
indeed
@PH13 What?
trained to be thirsty
15:29
@PH13 Haven't my guards taught you a lesson last night in the matrix?
like a fakir is trained to walk on coals etc
I'm wondering if you're serious.
maybe a little ;)
Common, make up a conversation.
about?
15:31
This is the last tough day for me. . .The last day when there are both Kung Fu classes and dry fasting.
@PH13 Something!
play clicker heroes
Huh?
o/ @Bon!
Seems there's less activity on meta these days.
I'm the devil for reinventing the visualization tag O:-)
MWAHHAHAHHHHAHAHAHAHAHA!
and I need another good question
today my question was in Computational Chemistry Daily
15:54
helowzz ...
hiho
hey @PH13 i got a little query on last day's topic.
suprise me
@inɒzɘmɒЯ.A.M how many mins remaining...
15:56
34?
i have started a demo run on my dft with 6-311+g* basis set, included the diffuse function too @PH13 could that be of help. ?
@diffracteD A lot.
BTW we're gonna go to an iftar party today. . . I might leave any minute.
@diffracteD that's what I told you last time :)
I was unsure about diffuse function ...
why?
15:59
will you guide me a bit with the importance of diffuse function ...
I got the polarization issue, you told about.
you know about the difference between STO and GTO?
no, not exactly..
STO is the minimal basis set, as I know.
maybe this helps you a little more than my explanations
you should read it, I think it is helpful
ok... going through...
when you're finished and I'm back from shopping I can help you with your following questions
so ... I'm a few minutes afk
16:47
so
and he's gone
 
1 hour later…
 
1 hour later…
19:05
I am back! (Oh no)
19:32
ಠ_ಠ
ಠ益ಠ
19:58
ಠ.ಠ
(ノಠ ∩ಠ)ノ彡( o°o)
20:13
ಠ_ಠ
(ノ-_-)ノ ~┻━┻ (/o\)
What's that?
ಠ_ಠ
(ノꐦ ⊙曲ఠ)ノ彡┻━┻
(ノꐦ ๑´Д`๑)ノ彡┻━┻
20:19
I know your little seekrit.
┻━┻ ︵ヽ(`Д´)ノ︵ ┻━┻
ಠ_ಠ
Still, the best is ಠ_ಠ.
ಠ_ಠ
(੭ ◕㉨◕)੭ =͟͟͞͞=͟͟͞͞三❆)’дº);,':=͟͟͞͞
≡/( .-.)\ ︵╰(«○»益«○»)╯︵ /(.□. /)̨
20:39
@inɒzɘmɒЯ.A.M wow imo-official.org/year_country_r.aspx?year=2015 iran did well
IMO we could do better, even with this corrupt darn system of education.
France is only 14 ;_;
germany is very bad o_o
@inɒzɘmɒЯ.A.M you are celebrating the atom-deal, too?
21:15
Atom-deal?
I don't know what the english term is ... that thing about the iranian atomic program
or nuclear program
Oh yeah. . .There have been fireworks here.
big party
People are so happy they're clogging the streets.
@PH13 Yep.
but don't use the nuclear rockets as fireworks
now the visualization is gone :)
21:25
Blows the steam off his shotgun

« first day (1174 days earlier)      last day (3510 days later) »