[CP2K:10076] Re: CP2K reads and writes the correct atomic coordinates
Matt W
mattwa... at gmail.com
Fri Mar 9 15:28:17 UTC 2018
Hi,
the pos file contains the coordinates _after_ one optimization step has
been made. I think your system makes an enormous jump because it is
initially massively unstable with massive forces.
Why this is I am not quite sure. Do atoms need to be centered in the cell
for MT poisson solver?
Matt
On Friday, March 9, 2018 at 1:31:50 PM UTC, David T wrote:
>
> 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
>>
>
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