<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">The input file “molecule.input” has a syntax error. The “&END KIND” for the “&KIND O” section is missing as indicated by the the indentation. Further issues are: (1) the pseudo potential for C should end with “q4”, (2) EPS_DEFAULT should be smaller, e.g. 1.0E-12, (3) the cutoff should be larger, e.g. 400 Ry, (4) CHO has an odd number of electrons which requires LSD.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">HTH<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="color:black">From: </span></b><span style="color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Hanaa Sari <hanaa.sarimohammed@gmail.com><br> <b>Date: </b>Tuesday, 1 October 2024 at 03:33<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>[CP2K:20733] Adsorption of organic molecules on metal surface<o:p></o:p></span></p> </div> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:36.0pt;line-height:11.75pt"> <span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#500050">Dear All,<o:p></o:p></span></p> <div style="margin-bottom:8.0pt"> <p class="MsoNormal" style="margin-left:36.0pt;line-height:11.75pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#500050">I am a new user of CP2K. <o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt;font-variant-ligatures:normal;font-variant-caps:normal;orphans:2;text-align:start;widows:2;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px"> <p class="MsoNormal" style="margin-left:36.0pt;line-height:11.75pt;background:white"> <span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A">I am trying to study the adsorption of organic molecules on metal surface. When I run the input file (in attachment) to optimize the molecule I have this message:<o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt;font-variant-ligatures:normal;font-variant-caps:normal;orphans:2;text-align:start;widows:2;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px"> <p class="MsoNormal" style="margin-left:36.0pt;line-height:11.75pt;background:white"> <span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A"><o:p> </o:p></span></p> </div> <div style="margin-bottom:8.0pt;font-variant-ligatures:normal;font-variant-caps:normal;orphans:2;text-align:start;widows:2;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px"> <p class="MsoNormal" style="margin-left:36.0pt;line-height:10.45pt;background:white"> <span style="font-size:7.5pt;font-family:"pg-1ff1",serif;color:black">i</span><span style="font-size:10.0pt;font-family:"pg-1ff1",serif;color:black">nvoking MPI_ABORT causes Open MPI to kill</span><span style="font-family:"Calibri",sans-serif;color:#26282A"><o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt;font-variant-ligatures:normal;font-variant-caps:normal;orphans:2;text-align:start;widows:2;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px"> <p class="MsoNormal" style="margin-left:36.0pt;line-height:10.45pt;background:white"> <span style="font-size:10.0pt;font-family:"pg-1ff1",serif;color:black"> all MPI processes.</span><span style="font-family:"Calibri",sans-serif;color:#26282A"><o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt;font-variant-ligatures:normal;font-variant-caps:normal;orphans:2;text-align:start;widows:2;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px"> <div style="margin-bottom:9.0pt;min-height:579.513px"> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;text-indent:-18.0pt;line-height:0%;mso-list:l0 level1 lfo1;background:white"> <![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span style="font-size:10.0pt;font-family:"pg-1ff1",serif;color:black">You may or may not see output from other processes, depending on</span><span style="font-family:"pg-1ff1",serif;color:black"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;line-height:0%;background:white"> <span style="font-size:10.0pt;font-family:"pg-1ff1",serif;color:black">exactly when Open MPI kills them</span><span style="font-family:"pg-1ff1",serif;color:black"><o:p></o:p></span></p> </div> </div> </div> </div> </div> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;text-indent:-18.0pt;line-height:0%;mso-list:l0 level1 lfo1;background:white"> <![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A">In the other side I </span><span style="font-size:10.5pt;font-family:Roboto;color:#26282A">try to optimize Ni(111) bulk and slab consisiting</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A"> layers </span><span style="font-family:"pg-1ff1",serif;color:black"><o:p></o:p></span></p> </div> <div> <div style="margin-bottom:8.0pt"> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;text-indent:-18.0pt;line-height:11.75pt;mso-list:l0 level1 lfo1;background:white"> <![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:#26282A"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A">and the only calculation that converge is that of the elementary cell . As soon as I increase the number of atoms the calculation do not converge.<o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt"> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;line-height:11.75pt;background:white"> <span style="font-size:10.5pt;font-family:Roboto;color:#26282A"> Could someone provide an example input file? </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A"> knowing that I am using the version cp2k 2024.1<o:p></o:p></span></p> </div> <div style="margin-bottom:8.0pt"> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;line-height:11.75pt;background:white"> <span style="font-size:10.5pt;font-family:Roboto;color:#26282A">Thank you.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#26282A"><o:p></o:p></span></p> </div> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:83.25pt;text-indent:-18.0pt;line-height:0%;mso-list:l0 level1 lfo1;background:white"> <![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span style="font-family:"pg-1ff1",serif;color:black"><o:p> </o:p></span></p> </div> </div> <div style="margin-bottom:8.0pt"> <p class="MsoNormal" style="margin-left:36.0pt;mso-line-height-alt:10.45pt"><span style="font-family:"Calibri",sans-serif;color:#26282A"><o:p> </o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/29df6ea1-a061-4ee5-af17-aa4cd407dee0n%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/29df6ea1-a061-4ee5-af17-aa4cd407dee0n%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </body> </html> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827FD87F7FBE1001384A562F4772%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827FD87F7FBE1001384A562F4772%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />