<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>     Mass
<br>
<br>        1     1 Co  27    3.108670    4.979180    4.103000     17.00 
<br>  58.9332
<br>        2     2 C    6    5.012420    5.338520    4.024640      4.00 
<br>  12.0107
<br>        3     3 O    8    6.120010    5.547740    3.979040      6.00 
<br>  15.9994
<br>        4     2 C    6    3.039780    4.921110    2.166350      4.00 
<br>  12.0107
<br>        5     3 O    8    2.999670    4.887060    1.039490      6.00 
<br>  15.9994
<br>        6     2 C    6    3.177500    5.036160    6.039690      4.00 
<br>  12.0107
<br>        7     3 O    8    3.217530    5.069060    7.166590      6.00 
<br>  15.9994
<br>        8     4 H    1    1.543250    4.684900    4.167410      1.00 
<br>   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>  58.9332
<br>        2     2 C    6    5.012420    5.338520    4.024640      4.00 
<br>  12.0107
<br>        3     3 O    8    6.120010    5.547740    3.979040      6.00 
<br>  15.9994
<br>        4     2 C    6    3.039780    4.921110    2.166350      4.00 
<br>  12.0107
<br>        5     3 O    8    2.999670    4.887060    1.039490      6.00 
<br>  15.9994
<br>        6     2 C    6    3.177500    5.036160    6.039690      4.00 
<br>  12.0107
<br>        7     3 O    8    3.217530    5.069060    7.166590      6.00 
<br>  15.9994
<br>        8     4 H    1    1.543250    4.684900    4.167410      1.00 
<br>   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>>     Full input deck please.
<br>> 
<br>>     On Friday, March 9, 2018 at 12:10:00 PM UTC, David T wrote:
<br>> 
<br>>         Dear all
<br>> 
<br>>         I am experiencing some very strange problem using CP2k v5.1
<br>> 
<br>>         This is the xyz I put in the input:
<br>> 
<br>>              &COORD
<br>>                  Co         3.10867        4.97918        4.10300
<br>>                  C          5.01242        5.33852        4.02464
<br>>                  O          6.12001        5.54774        3.97904
<br>>                  C          3.03978        4.92111        2.16635
<br>>                  O          2.99967        4.88706        1.03949
<br>>                  C          3.17750        5.03616        6.03969
<br>>                  O          3.21753        5.06906        7.16659
<br>>                  H          1.54325        4.68490        4.16741
<br>>              &END
<br>> 
<br>>         This is what CP2K reads and writes in the output:
<br>> 
<br>>           Co         0.0160950570       11.2078020944        4.0719885297
<br>>            C         3.4670167381        5.1560899034        4.0134146454
<br>>            O         6.1012882958        5.4441242537        4.0661997577
<br>>            C         1.2629748230        8.4349412628        2.0423121577
<br>>            O        -0.9667191619       19.0654343689        0.5979795609
<br>>            C         2.4935029798        5.7739885277        6.2317402018
<br>>            O         1.8313194493        5.1044335466        9.6405816871
<br>>            H        -1.4880140591        4.6452140486        4.2099725360
<br>> 
<br>> 
<br>>         What is going on?
<br>> 
<br>>         I am honestly lost. To me it seems some bug but I am sure it
<br>>         cannot be since it hasn't been reported yet.
<br>> 
<br>>         Thanks for helping
<br>>         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>