<div dir="ltr">Dear Tiziano<div><br></div><div>Thanks for helping and sorry for the confusion.</div><div>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. </div><div><br></div><div>However (and this was the reason I discovered the problem), if you look at the <font color="#ff0000">pos </font>file it is not. </div><div>So I wonder, what geometry is actually reading and dealing with?</div><div><br></div><div>In attachment all the files. </div><div><br></div><div>Best Regards</div><div>Davide</div><div><br></div><div><br></div><div><div><span style="font-size: 13px;">davide@Chiron:~/Downloads/tmp$ head test-read.xyz </span></div><div><span style="font-size: 13px;">    8</span></div><div><span style="font-size: 13px;"> i =    1, E =   -376.2828462525</span></div><div><span style="font-size: 13px;"> Co     3.10867    4.97918    4.10300</span></div><div><span style="font-size: 13px;"> C     5.01242    5.33852    4.02464</span></div><div><span style="font-size: 13px;"> O     6.12001    5.54774    3.97904</span></div><div><span style="font-size: 13px;"> C     3.03978    4.92111    2.16635</span></div><div><span style="font-size: 13px;"> O     2.99967    4.88706    1.03949</span></div><div><span style="font-size: 13px;"> C     3.17750    5.03616    6.03969</span></div><div><span style="font-size: 13px;"> O     3.21753    5.06906    7.16659</span></div><div><span style="font-size: 13px;"> H     1.54325    4.68490    4.16741</span></div></div><div><font color="#ff0000"><br></font></div><div><font color="#ff0000"><br></font></div><div><font color="#ff0000"><br></font></div><div><div><span style="font-size: 13px;"><font color="#ff0000">davide@Chiron:~/Downloads/tmp$ head test-read-pos-1.xyz </font></span></div><div><span style="font-size: 13px;"><font color="#ff0000">    8</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> i =    1, E =   -376.2828462525</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> Co     0.1124137270    10.9588831987    4.0824685674</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> C     3.5280570603    5.1635307543    4.0140373519</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> O     6.1062661101    5.4505588438    4.0622175172</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> C     1.2904350203    8.2758896120    2.0430686234</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> O    -0.8613815091    18.5193037422    0.6240682043</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> C     2.5026944563    5.7441422642    6.2256709056</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> O     2.1805270783    4.8495917826    9.7300549210</font></span></div><div><span style="font-size: 13px;"><font color="#ff0000"> H    -1.3613766597    4.6470224146    4.2074746843</font></span></div><div><br></div><div><br></div><div><br></div>On Friday, 9 March 2018 13:09:29 UTC, Tiziano Müller wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Dear Davide
<br>
<br>There seems to be a bit an inconsistency in the files you provided:
<br>
<br>The coordinate section can't be in an XYZ file (CP2K will fail while
<br>parsing it).
<br>
<br>Now, when I enter the coordinates you mention into an XYZ file, CP2K
<br>gives me:
<br>
<br>  Atom  Kind  Element    X      Y      Z      Z(eff)
<br>Â Â Â Mass
<br>
<br>    1   1 Co  27   3.108670   4.979180   4.103000   17.00
<br>Â 58.9332
<br>Â Â Â Â 2 Â Â 2 C Â Â 6 Â Â 5.012420 Â Â 5.338520 Â Â 4.024640 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 3 Â Â 3 O Â Â 8 Â Â 6.120010 Â Â 5.547740 Â Â 3.979040 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 4 Â Â 2 C Â Â 6 Â Â 3.039780 Â Â 4.921110 Â Â 2.166350 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 5 Â Â 3 O Â Â 8 Â Â 2.999670 Â Â 4.887060 Â Â 1.039490 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 6 Â Â 2 C Â Â 6 Â Â 3.177500 Â Â 5.036160 Â Â 6.039690 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 7 Â Â 3 O Â Â 8 Â Â 3.217530 Â Â 5.069060 Â Â 7.166590 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 8 Â Â 4 H Â Â 1 Â Â 1.543250 Â Â 4.684900 Â Â 4.167410 Â Â Â 1.00
<br>Â Â 1.0079
<br>
<br>which looks correct.
<br>
<br>Also, when I put the &COORD section you provided in the provided input
<br>file instead of the &TOPOLOGY, I get:
<br>
<br>    1   1 Co  27   3.108670   4.979180   4.103000   17.00
<br>Â 58.9332
<br>Â Â Â Â 2 Â Â 2 C Â Â 6 Â Â 5.012420 Â Â 5.338520 Â Â 4.024640 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 3 Â Â 3 O Â Â 8 Â Â 6.120010 Â Â 5.547740 Â Â 3.979040 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 4 Â Â 2 C Â Â 6 Â Â 3.039780 Â Â 4.921110 Â Â 2.166350 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 5 Â Â 3 O Â Â 8 Â Â 2.999670 Â Â 4.887060 Â Â 1.039490 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 6 Â Â 2 C Â Â 6 Â Â 3.177500 Â Â 5.036160 Â Â 6.039690 Â Â Â 4.00
<br>Â 12.0107
<br>Â Â Â Â 7 Â Â 3 O Â Â 8 Â Â 3.217530 Â Â 5.069060 Â Â 7.166590 Â Â Â 6.00
<br>Â 15.9994
<br>Â Â Â Â 8 Â Â 4 H Â Â 1 Â Â 1.543250 Â Â 4.684900 Â Â 4.167410 Â Â Â 1.00
<br>Â Â 1.0079
<br>
<br>Which also seems ok.
<br>
<br>Best regards,
<br>Tiziano
<br>
<br>On 09.03.2018 13:44, David T wrote:
<br>> Dear Mat
<br>>
<br>> thanks for answering. I attached the full input.
<br>>
<br>> Best Regards
<br>> Davide
<br>>
<br>> On Friday, 9 March 2018 12:32:56 UTC, Matt W wrote:
<br>>
<br>> Â Â Full input deck please.
<br>>
<br>> Â Â On Friday, March 9, 2018 at 12:10:00 PM UTC, David T wrote:
<br>>
<br>> Â Â Â Â Dear all
<br>>
<br>> Â Â Â Â I am experiencing some very strange problem using CP2k v5.1
<br>>
<br>> Â Â Â Â This is the xyz I put in the input:
<br>>
<br>> Â Â Â Â Â Â Â &COORD
<br>>          Co     3.10867    4.97918    4.10300
<br>> Â Â Â Â Â Â Â Â Â CÂ Â Â Â Â 5.01242Â Â Â Â 5.33852Â Â Â Â 4.02464
<br>> Â Â Â Â Â Â Â Â Â OÂ Â Â Â Â 6.12001Â Â Â Â 5.54774Â Â Â Â 3.97904
<br>> Â Â Â Â Â Â Â Â Â CÂ Â Â Â Â 3.03978Â Â Â Â 4.92111Â Â Â Â 2.16635
<br>> Â Â Â Â Â Â Â Â Â OÂ Â Â Â Â 2.99967Â Â Â Â 4.88706Â Â Â Â 1.03949
<br>> Â Â Â Â Â Â Â Â Â CÂ Â Â Â Â 3.17750Â Â Â Â 5.03616Â Â Â Â 6.03969
<br>> Â Â Â Â Â Â Â Â Â OÂ Â Â Â Â 3.21753Â Â Â Â 5.06906Â Â Â Â 7.16659
<br>> Â Â Â Â Â Â Â Â Â HÂ Â Â Â Â 1.54325Â Â Â Â 4.68490Â Â Â Â 4.16741
<br>> Â Â Â Â Â Â Â &END
<br>>
<br>> Â Â Â Â This is what CP2K reads and writes in the output:
<br>>
<br>>       Co     0.0160950570    11.2078020944    4.0719885297
<br>> Â Â Â Â Â Â CÂ Â Â Â Â 3.4670167381Â Â Â Â 5.1560899034Â Â Â Â 4.0134146454
<br>> Â Â Â Â Â Â OÂ Â Â Â Â 6.1012882958Â Â Â Â 5.4441242537Â Â Â Â 4.0661997577
<br>> Â Â Â Â Â Â CÂ Â Â Â Â 1.2629748230Â Â Â Â 8.4349412628Â Â Â Â 2.0423121577
<br>> Â Â Â Â Â Â OÂ Â Â Â -0.9667191619Â Â Â Â 19.0654343689Â Â Â Â 0.5979795609
<br>> Â Â Â Â Â Â CÂ Â Â Â Â 2.4935029798Â Â Â Â 5.7739885277Â Â Â Â 6.2317402018
<br>> Â Â Â Â Â Â OÂ Â Â Â Â 1.8313194493Â Â Â Â 5.1044335466Â Â Â Â 9.6405816871
<br>> Â Â Â Â Â Â HÂ Â Â Â -1.4880140591Â Â Â Â 4.6452140486Â Â Â Â 4.2099725360
<br>>
<br>>
<br>> Â Â Â Â What is going on?
<br>>
<br>> Â Â Â Â I am honestly lost. To me it seems some bug but I am sure it
<br>> Â Â Â Â cannot be since it hasn't been reported yet.
<br>>
<br>> Â Â Â Â Thanks for helping
<br>> Â Â Â Â Davide
<br>>
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<br>
<br>--
<br>Tiziano Müller
<br>University of Zurich
<br>Department of Chemistry
<br>Winterthurerstrasse 190
<br>CH-8057 Zürich
<br>
<br>Tel: +41 44 63 54234
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<br></blockquote></div></div>