<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>>
<br>> --
<br>> You received this message because you are subscribed to the Google
<br>> Groups "cp2k" group.
<br>> To unsubscribe from this group and stop receiving emails from it, send
<br>> an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="_Mf2Y8wCBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@googlegroups.<wbr>com</a>
<br>> <mailto:<a href="javascript:" target="_blank" gdf-obfuscated-mailto="_Mf2Y8wCBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@<wbr>googlegroups.com</a>>.
<br>> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="_Mf2Y8wCBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>
<br>> <mailto:<a href="javascript:" target="_blank" gdf-obfuscated-mailto="_Mf2Y8wCBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>><wbr>.
<br>> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/group/cp2k';return true;" onclick="this.href='https://groups.google.com/group/cp2k';return true;">https://groups.google.com/<wbr>group/cp2k</a>.
<br>> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/<wbr>optout</a>.
<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
<br><a href="http://www.chem.uzh.ch" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;">www.chem.uzh.ch</a>
<br><a href="javascript:" target="_blank" gdf-obfuscated-mailto="_Mf2Y8wCBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">tizia...@chem.uzh.ch</a>
<br></blockquote></div></div>