Re: [cclib-users] A question about LPA

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Hi Adam,

No, as long as the symmetry is not Oh or Td, there is no warning.

Best,
Martin

On Tue, Nov 15, 2011 at 12:22 PM, Adam Tenderholt <ate...@gm...>wrote:

> Hi Martin,
>
> Thanks for the info. It's a bit odd that slight distortions return the
> value to 70.00. Out of curiosity, do you still get the complex warning
> at the LPA step for these calculations?
>
> Adam
>
>
> On Tue, Nov 15, 2011 at 11:50 AM, Martin Rahm <mar...@gm...>
> wrote:
> > Hi Adam, and everyone,
> > I just figured out a way around the problem. First, the same thing
> happens
> > for single points, and it remains if one runs with "nosymm", or if the
> > nuclear coordinate input is switched between cartesian/z-mat. However,
> these
> > latter changes do seem to affect the total number of electrons and the
> > orbital populations slightly different.
> > The solution I found was to perturb the Oh symmetry very slightly (into
> > C3v), then the electron count becomes 70.000, and all ligands are treated
> > equally. The same goes for Td systems, which have to be disturbed into
> D2d.
> > In other words it seems like the code has problems with "spherically"
> > symmetric wave functions.
> > Best,
> > Martin
> >
> >
> > On Tue, Nov 15, 2011 at 10:19 AM, Adam Tenderholt <ate...@gm...
> >
> > wrote:
> >>
> >> Hi Martin and others,
> >>
> >> Sorry for the delayed response....
> >>
> >> The complex warning suggests there's a complex value being discarded
> >> that may be important. Does anyone know if we should be taking the
> >> norm instead of simply discarding the imaginary part?
> >>
> >> Also, does it matter that this is an Opt Freq calc? Does Gaussian
> >> print the one-electron overlap matrix (aooverlaps) at the final
> >> geometry? (I usually don't combine Opt and Freq calcs, so I don't
> >> know, but the file looks like the final overlap matrix isn't at the
> >> converged geometry.) If not, perhaps the problem is from using the
> >> overlap matrix at the first structure and the orbital coefficients at
> >> the final structure.
> >>
> >> Take care,
> >>
> >> Adam
> >>
> >> On Sat, Nov 5, 2011 at 1:20 PM, Martin Rahm <mar...@gm...>
> wrote:
> >> > Hi Karol,
> >> > I realized that I had used cartesian coordinates in the original input
> >> > file.
> >> > When I used a z-matrix instead (and defined S as atom 0) the LPA
> warning
> >> > was
> >> > still the same, but the total number of electrons turned out to be
> 70.22
> >> > (instead of 70.3).
> >> > I should also mention that the LPA-charge of all F ligands are
> slightly
> >> > different, even though they are symmetrically identical.
> >> > Best,
> >> > Martin
> >> > On Sat, Nov 5, 2011 at 1:34 AM, Karol M. Langner
> >> > <kar...@gm...>
> >> > wrote:
> >> >>
> >> >> Hi Martin,
> >> >>
> >> >> Can you provide the output file for that Gaussian job?
> >> >>
> >> >> Best,
> >> >> Karol
> >> >>
> >> >> On Nov 04 2011, Martin Rahm wrote:
> >> >> > Dear List,
> >> >> >
> >> >> > I'm running a trial Löwdin population analysis (LPA) on SF6, from a
> >> >> >  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
> >> >> > electrons gets overestimated by 0.3 (70.3), and there is a "complex
> >> >> > warning" when running the LPA.
> >> >> >
> >> >> > LPA is supposed to be rotationally invariant if one use "pure"
> >> >> > spherical
> >> >> > harmonics in the basis set, e.g. 5 d functions instead of 6. (which
> >> >> > cc-pVTZ
> >> >> > does). Anyone have any clue to this behavior?
> >> >> >
> >> >> > Best regards,
> >> >> > Martin
> >> >> >
> >> >> > Gaussian Input: ---------
> >> >> > # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
> >> >> >
> >> >> > Title Card Required
> >> >> >
> >> >> > 0 1
> >> >> >  F                  0.00000000    0.00000000    1.57972200
> >> >> >  F                  0.00000000    1.57972200    0.00000000
> >> >> >  F                  0.00000000    0.00000000   -1.57972200
> >> >> >  F                  0.00000000   -1.57972200    0.00000000
> >> >> >  F                  1.57972200    0.00000000    0.00000000
> >> >> >  F                 -1.57972200    0.00000000    0.00000000
> >> >> >  S                  0.00000000    0.00000000    0.00000000
> >> >> >
> >> >> > Python script: --------
> >> >> > from numpy import *
> >> >> > from cclib.parser import ccopen
> >> >> > from cclib.method import LPA
> >> >> > parser = ccopen("test.log")
> >> >> > data = parser.parse()
> >> >> > method = LPA(data)
> >> >> > method.calculate()
> >> >> >
> >> >> >
> >> >> >
> savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
> >> >> >
> >> >> > Script output: --------
> >> >> > ...
> >> >> > [Gaussian test.log INFO] Creating attribute coreelectrons[]
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO]
> Creating
> >> >> > attribute aoresults: [array[2]]
> >> >> >
> >> >> >
> >> >> >
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> >> >> > ComplexWarning: Casting complex values to real discards the
> imaginary
> >> >> > part
> >> >> >   self.aoresults[spin][i] = numpy.multiply(temp1,
> temp2).astype("d")
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
> >> >> > partitioned results in fragresults: [array[2]]
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO]
> Creating
> >> >> > fragcharges: array[1]
> >> >>
> >> >> >
> >> >> >
> >> >> >
> ------------------------------------------------------------------------------
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> >> >>
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> >> >>
> >> >>
> >> >> --
> >> >> written by Karol Langner
> >> >> Sat Nov  5 09:34:29 CET 2011
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
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> >> >
> >
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