Re: possibly a bug: no spin multiplicity in S, K

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Re: possibly a bug: no spin multiplicity in S, K

NakataMaho
Hi Open BABEL developers,

Following bug report is raised as
https://github.com/openbabel/openbabel/issues/340

Best,
 Nakata Maho

From: NakataMaho <[hidden email]>
Subject: possibly a bug: no spin multiplicity in S, K
Date: Mon, 12 Sep 2016 12:04:20 +0900 (JST)

> Dear Open babel developers,
>
> following is also wrong. Total spin should not be odd number as S- has 17 electrons.
>
> obabel -:"[S-]" -oreport
> FILENAME:
> FORMULA: S-
> MASS: 32.0650
> EXACT MASS: 31.9720710
> TOTAL CHARGE: -1
> TOTAL SPIN: 3
>
> K do not output total spin and it should. I think it is doublet.
> $ obabel -:"[K]" -oreport
> FILENAME:
> FORMULA: K
> MASS: 39.0983
> EXACT MASS: 38.9637067
> INTERATOMIC DISTANCES
>
> following is also wrong. AlO has 13+8 electrons and total spin should not be an odd number.
> $ obabel -:"O=[Al]" -oreport
> FILENAME:
> FORMULA: AlO
> MASS: 42.9809
> EXACT MASS: 42.9764532
> TOTAL SPIN: 3
>
> following is also wrong. PH2- has 18 electrons and total spin should not be an even number.
> 15 + 2 + 1 = 18 electrons
> $ obabel -:"[PH2-]" -oreport
> ....
> TOTAL SPIN: 2
>
> following is also wrong. Sc has 21 electrons and an even number total spin.
> $ obabel -:"[Sc]" -oreport
> FILENAME:
> FORMULA: Sc
> MASS: 44.9559
> EXACT MASS: 44.9559119
> INTERATOMIC DISTANCES
> ..
>
> following is also wrong. C[Si+] has 22 electrons and should have an odd number total spin.
> $ obabel -:"C[Si+]" -oreport
> FILENAME:
> FORMULA: CH3Si+
> MASS: 43.1200
> EXACT MASS: 43.0004016
> TOTAL CHARGE: 1
> TOTAL SPIN: 4
>
> .....
>
> Best,
>  Nakata Maho
>
> From: NakataMaho <[hidden email]>
> Subject: Re: possibly a bug: no spin multiplicity in Na
> Date: Mon, 12 Sep 2016 11:40:46 +0900 (JST)
>
>> Dear open babel developers,
>>
>> $ obabel -:"[Na]" -oreport
>> $ obabel -:"[Be].[Na]" -oreport
>> should print "TOTAL SPIN: 2"
>> as well.
>>
>> Best,
>>  Nakata Maho
>>
>> From: NakataMaho <[hidden email]>
>> Subject: Re: possibly a bug: no spin multiplicity in B
>> Date: Mon, 12 Sep 2016 11:35:11 +0900 (JST)
>>
>>> Dear open babel developers,
>>>
>>> following out is also seems to be wrong.
>>> total spin should be singlet, triplet ...  as B- has 6 electrons
>>>
>>> $ obabel -:"[B-]" -oreport
>>> FILENAME:
>>> FORMULA: B-
>>> MASS: 10.8110
>>> EXACT MASS: 11.0093054
>>> TOTAL CHARGE: -1
>>> TOTAL SPIN: 4
>>>
>>> Best,
>>>  Nakata Maho
>>>
>>> From: NakataMaho <[hidden email]>
>>> Subject: Re: possibly a bug: no spin multiplicity in Li
>>> Date: Mon, 12 Sep 2016 11:31:24 +0900 (JST)
>>>
>>>> Dear open babel developers,
>>>>
>>>> I found possibly a bug in open babel.
>>>> for Li, "TOTAL SPIN: 2"  is missing
>>>> ------------------------
>>>> $ obabel -:"[Li]" -oreport
>>>> FILENAME:
>>>> FORMULA: Li
>>>> MASS: 6.9410
>>>> EXACT MASS: 7.0160045
>>>> INTERATOMIC DISTANCES
>>>> ------------------------
>>>> whereas
>>>> $ obabel -:"[H]" -oreport
>>>> FILENAME:
>>>> FORMULA: H
>>>> MASS: 1.0079
>>>> EXACT MASS: 1.0078250
>>>> TOTAL SPIN: 2
>>>> ------------------------
>>>>
>>>> I'm using
>>>> $ obabel
>>>> No input file or format spec or possibly a misplaced option.
>>>> Most options must come after the input files. (-i -o -O -m can be anywhwere.)
>>>>
>>>> Open Babel 2.3.90 -- Sep  9 2016 -- 13:30:54
>>>> Usage:
>>>> obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
>>>> Try  -H option for more information.
>>>>
>>>> Best,
>>>>  Nakata Maho
>>>>

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