[CP2K:10076] Re: CP2K reads and writes the correct atomic coordinates
David T
amazing... at gmail.com
Fri Mar 9 13:31:50 UTC 2018
Dear Tiziano
Thanks for helping and sorry for the confusion.
That was a test I did before posting. I confirm that using reading from a
xyz file in cp2k output the geometry is reported correctly.
However (and this was the reason I discovered the problem), if you look at
the pos file it is not.
So I wonder, what geometry is actually reading and dealing with?
In attachment all the files.
Best Regards
Davide
davide at Chiron:~/Downloads/tmp$ head test-read.xyz
8
i = 1, E = -376.2828462525
Co 3.10867 4.97918 4.10300
C 5.01242 5.33852 4.02464
O 6.12001 5.54774 3.97904
C 3.03978 4.92111 2.16635
O 2.99967 4.88706 1.03949
C 3.17750 5.03616 6.03969
O 3.21753 5.06906 7.16659
H 1.54325 4.68490 4.16741
davide at Chiron:~/Downloads/tmp$ head test-read-pos-1.xyz
8
i = 1, E = -376.2828462525
Co 0.1124137270 10.9588831987 4.0824685674
C 3.5280570603 5.1635307543 4.0140373519
O 6.1062661101 5.4505588438 4.0622175172
C 1.2904350203 8.2758896120 2.0430686234
O -0.8613815091 18.5193037422 0.6240682043
C 2.5026944563 5.7441422642 6.2256709056
O 2.1805270783 4.8495917826 9.7300549210
H -1.3613766597 4.6470224146 4.2074746843
On Friday, 9 March 2018 13:09:29 UTC, Tiziano Müller wrote:
>
> Dear Davide
>
> There seems to be a bit an inconsistency in the files you provided:
>
> The coordinate section can't be in an XYZ file (CP2K will fail while
> parsing it).
>
> Now, when I enter the coordinates you mention into an XYZ file, CP2K
> gives me:
>
> Atom Kind Element X Y Z Z(eff)
> Mass
>
> 1 1 Co 27 3.108670 4.979180 4.103000 17.00
> 58.9332
> 2 2 C 6 5.012420 5.338520 4.024640 4.00
> 12.0107
> 3 3 O 8 6.120010 5.547740 3.979040 6.00
> 15.9994
> 4 2 C 6 3.039780 4.921110 2.166350 4.00
> 12.0107
> 5 3 O 8 2.999670 4.887060 1.039490 6.00
> 15.9994
> 6 2 C 6 3.177500 5.036160 6.039690 4.00
> 12.0107
> 7 3 O 8 3.217530 5.069060 7.166590 6.00
> 15.9994
> 8 4 H 1 1.543250 4.684900 4.167410 1.00
> 1.0079
>
> which looks correct.
>
> Also, when I put the &COORD section you provided in the provided input
> file instead of the &TOPOLOGY, I get:
>
> 1 1 Co 27 3.108670 4.979180 4.103000 17.00
> 58.9332
> 2 2 C 6 5.012420 5.338520 4.024640 4.00
> 12.0107
> 3 3 O 8 6.120010 5.547740 3.979040 6.00
> 15.9994
> 4 2 C 6 3.039780 4.921110 2.166350 4.00
> 12.0107
> 5 3 O 8 2.999670 4.887060 1.039490 6.00
> 15.9994
> 6 2 C 6 3.177500 5.036160 6.039690 4.00
> 12.0107
> 7 3 O 8 3.217530 5.069060 7.166590 6.00
> 15.9994
> 8 4 H 1 1.543250 4.684900 4.167410 1.00
> 1.0079
>
> Which also seems ok.
>
> Best regards,
> Tiziano
>
> On 09.03.2018 13:44, David T wrote:
> > Dear Mat
> >
> > thanks for answering. I attached the full input.
> >
> > Best Regards
> > Davide
> >
> > On Friday, 9 March 2018 12:32:56 UTC, Matt W wrote:
> >
> > Full input deck please.
> >
> > On Friday, March 9, 2018 at 12:10:00 PM UTC, David T wrote:
> >
> > Dear all
> >
> > I am experiencing some very strange problem using CP2k v5.1
> >
> > This is the xyz I put in the input:
> >
> > &COORD
> > Co 3.10867 4.97918 4.10300
> > C 5.01242 5.33852 4.02464
> > O 6.12001 5.54774 3.97904
> > C 3.03978 4.92111 2.16635
> > O 2.99967 4.88706 1.03949
> > C 3.17750 5.03616 6.03969
> > O 3.21753 5.06906 7.16659
> > H 1.54325 4.68490 4.16741
> > &END
> >
> > This is what CP2K reads and writes in the output:
> >
> > Co 0.0160950570 11.2078020944
> 4.0719885297
> > C 3.4670167381 5.1560899034
> 4.0134146454
> > O 6.1012882958 5.4441242537
> 4.0661997577
> > C 1.2629748230 8.4349412628
> 2.0423121577
> > O -0.9667191619 19.0654343689
> 0.5979795609
> > C 2.4935029798 5.7739885277
> 6.2317402018
> > O 1.8313194493 5.1044335466
> 9.6405816871
> > H -1.4880140591 4.6452140486
> 4.2099725360
> >
> >
> > What is going on?
> >
> > I am honestly lost. To me it seems some bug but I am sure it
> > cannot be since it hasn't been reported yet.
> >
> > Thanks for helping
> > Davide
> >
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> --
> Tiziano Müller
> University of Zurich
> Department of Chemistry
> Winterthurerstrasse 190
> CH-8057 Zürich
>
> Tel: +41 44 63 54234
> www.chem.uzh.ch
> tizia... at chem.uzh.ch <javascript:>
>
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