Re: [cclib-users] A question about LPA

[Adam T. <ate...@gm...>]

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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>>
>> --
>> written by Karol Langner
>> Sat Nov  5 09:34:29 CET 2011
>
>
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