<div>Dear Kazimieras</div><div>Please forgive me if I am asking very general stupid questions.</div><div>I am a newbie of cp2k. Could you tell me how to do with TOPOLOGY section? which file format should I add? PDB , PSF or what others？</div><div><br></div><div> Best regards<br>Vaclav</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">在2019年9月11日星期三 UTC+8 下午4:31:37&...@gmail.com> 写道：<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr">Input file specified atomic coordinates and topology section, which was absent in my input file. That was a thing that caused the error. Sorry for interrupting.<div>Regards,</div><div> Kazimieras<br><div><br></div></div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 11, 2019 at 11:15 AM kazimieras tamoliunas <<a href data-email-masked rel="nofollow">k....@gmail.com</a>> wrote:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello,<div> i'm trying to restart geometry optimisation after maximum number of optimisation steps was reached, without reaching threshold values. I'm trying to restart a calculation from<font color="#000000" style="background-color:rgb(255,255,255)"> *<span style="font-family:"Andale Mono";font-size:12px">-1.restart.bak-3 </span></font>input file, but i run into this CPASSERT problem: </div><div><br></div><div><p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> *******************************************************************************</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * ___ *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * / \ *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * [ABORT] *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * \___/ CPASSERT failed *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * | *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * O/| *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * /| | *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> * / \ atoms_input.F:121 *</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> *******************************************************************************</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono";min-height:14px"><span style="background-color:rgb(255,255,255)"><font color="#000000"><span style="font-variant-ligatures:no-common-ligatures"></span><br></font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono";min-height:14px"><span style="background-color:rgb(255,255,255)"><font color="#000000"><span style="font-variant-ligatures:no-common-ligatures"></span><br></font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> ===== Routine Calling Stack =====</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono";min-height:14px"><span style="background-color:rgb(255,255,255)"><font color="#000000"><span style="font-variant-ligatures:no-common-ligatures"></span><br></font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> 5 read_atoms_input</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> 4 coordinate_control_READ_COORDINATE</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> 3 coordinate_control</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> 2 topology_control</font></span></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"> 1 CP2K</font></span></p><p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale Mono""><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(255,255,255)"><font color="#000000"><br></font></span></p><p style="font-stretch:normal;line-height:normal"> I'm asking because there is no apparent reason for this behaviour. If i start the calculation from my own input file, everything goes well. Maybe someone has a clue of why is this happening?<br></p><p style="font-stretch:normal;line-height:normal"><br></p><p style="font-stretch:normal;line-height:normal">Regards,</p><p style="font-stretch:normal;line-height:normal"> Kazimieras Tamoliūnas</p></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div></div>
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