[molpro-user] Bad Localized Orbitals?

Gerald Knizia knizia at theochem.uni-stuttgart.de
Mon Feb 13 18:13:11 CET 2017


Dear Matthias,
you could try using IboView (www.iboview.org) for visualization. Apart
from making prettier pictures, it also automatically derives reasonable
iso values by determining the iso values in such a away that they
enclose 80% of the electron's density (or any other threshold you set
up).

Regarding the localization: I think the localization defaults to Pipek-
Mezey. If you want interpretable orbitals, it might be better to switch
to IBO, like this:

{df-rhf}
{ibba}  ! intrinsic basis bonding analysis (makes IBO localized
orbitals)

Best wishes,
Gerald

On Fri, 2017-02-10 at 12:45 -0700, Matthias Heger wrote:
> Dear Peter,
> 
> thank you for your reply! After looking through your files and
> seeing 
> the same thing, I finally realized that the problem was actually
> very 
> mundane. The two cube files default to the unfortunate isovalues of 
> about 0.103 and 0.013 in Chimera, and it seems I didn't pay close
> enough 
> attention to spot the difference between those numbers.
> 
> So, everything is ok. No reason to worry.
> 
> Best,
> Matthias
> 
> --
> Dr. Matthias Heger
> Department of Chemistry, University of Alberta
> 11227 Saskatchewan Drive NW
> Edmonton, AB T6G 2G2, Canada
> 
> Office: CCIS 4-151
> Email: heger at ualberta.ca
> 
> Am 10-Feb-2017 um 11:23 AM schrieb Peter Knowles:
> > I can’t reproduce this problem at all. I get solid localised
> > orbitals 3.1 and 4.1, visualising either the cube files with VMD,
> > or (more easily) generating a molden file and using jmol. Please
> > have a look at the files in
> > https://www.odrive.com/s/252b3e9c-8f69-4875-8f2d-063b88e503ed-589e0
> > 2ca
> > 
> > Best regards,
> > Peter Knowles
> > 
> > > On 9 Feb 2017, at 21:26, Matthias Heger <heger at ualberta.ca>
> > > wrote:
> > > 
> > > Hello everyone,
> > > 
> > > I've been doing a quick LMP2 calculation in Molpro 2015.1 on
> > > formaldehyde. My input is fairly straightforward, and attached to
> > > the end of this email. With NPASEL=0.07, the domain definitions
> > > in the output look like this:
> > > 
> > >   Orb.   Atom     Charge      Total
> > >   3.1    2 C       1.11
> > >          4 H       0.88        1.99
> > >   4.1    2 C       1.11
> > >          3 H       0.88        1.99
> > >   5.1    1 O       1.31
> > >          2 C       0.68        2.00
> > >   6.1    1 O       1.36
> > >          2 C       0.64        2.00
> > >   7.1    1 O       1.91        1.91
> > >   8.1    1 O       1.97        1.97
> > > 
> > > When visualizing the localized orbitals, #4.1 looks like I would
> > > expect a localized C-H bond orbital to turn out. However,
> > > something bad seems to be going on with orbital 3.1:
> > > http://i.imgur.com/JJn1Kwl.png
> > > I noticed something similar happening in pentane. The C-H bond
> > > orbitals on one end of the molecule looked fine, while those on
> > > the other end were quite messy.
> > > 
> > > Does anyone know what's going on here? How will this impact my
> > > correlation energies?
> > > 
> > > Best,
> > > Matthias
> > > 
> > > 
> > > ***
> > > basis=vtz
> > > angstrom
> > > geomtyp=xyz
> > > orient,mass
> > > symmetry,nosym
> > > geometry={
> > >    4
> > > fa
> > > O          0.0000000000        0.0000000000        0.6034321216
> > > C          0.0000000000        0.0000000000       -0.6053608971
> > > H          0.0000000000        0.9357726712       -1.1823928760
> > > H          0.0000000000       -0.9357726712       -1.1823928760}
> > > df-hf
> > > {df-lmp2
> > > local,npasel=0.07,savorb=3000.2}
> > > {cube,Formaldehyde_loc
> > > orbital,occ,record=3000.2,type=local}
> > > 
> > > --
> > > Dr. Matthias Heger
> > > Department of Chemistry, University of Alberta
> > > 11227 Saskatchewan Drive NW
> > > Edmonton, AB T6G 2G2, Canada
> > > 
> > > Office: CCIS 4-151
> > > Email: heger at ualberta.ca
> > > _______________________________________________
> > > Molpro-user mailing list
> > > Molpro-user at molpro.net
> > > http://www.molpro.net/mailman/listinfo/molpro-user
> > 
> > --
> > Prof. Peter J. Knowles
> > School of Chemistry, Cardiff University, Main Building, Park Place,
> > Cardiff CF10 3AT, UK
> > Telephone: +44 29 208 79182
> > Email: KnowlesPJ at Cardiff.ac.uk
> > 
> > Yr Athro Peter J. Knowles
> > Yr Ysgol Cemeg, Prifysgol Caerdydd,
> > Prif Adeilad, Plas y Parc
> > Caerdydd CF10 3AT, DU
> > Ffôn: +44 2920 879182
> > Ebost: KnowlesPJ at Caerdydd.ac.uk
> > Ysgrifennwch ataf yn Gymraeg neu Saesneg
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> 
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