Thank you very much.<br><br>I really appreciate it.<br><br>I'll try to modify and rerun my job.<br><br><br><div class="gmail_quote">On Wed, Nov 21, 2012 at 10:36 PM, shoutian sun <span dir="ltr"><<a href="mailto:sunshou...@yahoo.com.cn" target="_blank">sunshou...@yahoo.com.cn</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:14pt;font-family:新宋体,nsimsun,sans-serif"><div><span>Hi <font face="Arial">SeokYun,</font></span></div>
<div><span><font face="Arial"></font>I have some <a href="http://cn.mg20.mail.yahoo.com/search?hl=zh-CN&safe=strict&tbo=d&biw=1397&bih=740&spell=1&q=suggestions&sa=X&ei=X5etUM2zKvGOiAfbpYGABA&ved=0CCsQBSgA" target="_blank"><font color="#cc0033">suggestions</font></a> for your input file.</span></div>
<div><span style="font-size:13px;font-family:arial"></span> </div><div><span style="font-size:13px;font-family:arial">1. The conformer you used for optimization is very poor, even using atomic unit,</span></div><div><span style="font-size:13px;font-family:arial"><span> the C-C distance of the ring is about 3.33 anstrom (kinds be wrong) or 3.33 bohr </span></span></div>
<div><span style="font-size:13px;font-family:arial"><span><span> </span>(about 1.76 angstrom, also a bit larger, isn't it?). So, my <a href="http://cn.mg20.mail.yahoo.com/search?hl=zh-CN&safe=strict&tbo=d&biw=1397&bih=740&spell=1&q=suggestions&sa=X&ei=X5etUM2zKvGOiAfbpYGABA&ved=0CCsQBSgA" target="_blank"><font color="#cc0033">suggestion</font></a> is rebuilding</span></span></div>
<div><span style="font-size:13px;font-family:arial"><span><span> your
conformer.</span></span></span></div><div><span style="font-size:13px;font-family:arial"><span><span></span></span></span> </div><div><span style="font-size:13px;font-family:arial"><span><span>2. use the POISSON_SOLVER (I think your systerm is a cluster, right?)</span></span></span></div>
<div style="font-family:新宋体,nsimsun,sans-serif;font-size:14pt"><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div><div> &POISSON<br> <span> </span> PERIODIC none<br> <span> </span> POISSON_SOLVER wavelet<br>
&END POISSON<br></div><div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">3. use MINIMIZER CG for OT sec. (If SCF doesn't converge, sometimes, it works)</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">4. XC_FUNCTIONAL Pade is not a good choice. (BLYP, I always used.)</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">5. sometime, SCF doesn't converge, you have to use smooth method in the &XC section</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> </span>, as follows:</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span> &XC_GRID <br> XC_SMOOTH_RHO NN10<br> XC_DERIV SPLINE2_SMOOTH<br>
&END XC_GRID </span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><br>6. cell parameter:</span> ABC 40.000 40.000 40.000</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> I think the default unit is angstrom, right?</span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span> 40.0 angstrom for 35 atoms conformer is quite big.</span></span></div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span><span> And very time consuming, Don't you think so?</span></span></span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span><span><span><span> (PERIODIC none for clusters.)</span></span></span></span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span><span></span></span></span> </div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">7. The coordinates of your conformer. I think your comformer</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> is build in atomic unit. And you do not modify it and just put</span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span> it in the &COORD.....&END COORD section. Am I right?</span></span></div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span><span> However, the problem is the default unit of atom coordinates</span></span></span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span><span><span><span> for cp2k is angstrom, not bohr. So, please modify it, or add</span></span></span></span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span><span><span><span> key word: <font face="Courier New">UNIT Bohr in the following sec.</font></span></span></span></span></span></div>
<div class="im"><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span><span><span><span><span><font face="Courier New"></font></span></span></span></span></span> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> </span>&COORD</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span> <span> </span></span>C 15.02103029 <a href="tel:21.43572257" value="+12143572257" target="_blank">21.43572257</a> <a href="tel:20.18000314" value="+12018000314" target="_blank">20.18000314</a></div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span> <span> </span></span>C 12.13797029 19.86029257 20.10217314</div></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> <span> <span> </span></span></span>..................</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> <span> </span> &END COORD</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">8. using POISSON_SOLVER wavelet, you have to use the following key words</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
<span> to put the cluster in the center of the box.</span></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"><span></span> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
&TOPOLOGY<br> &CENTER_COORDINATES <br> &END<br> &END <br></div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
I rebuild your comformer and do the optimization with my input file, it converge well.</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">For detail, please refer to cp2k input reference.</div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">Hope, it works for you.</div>
<div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">Regards,</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
sun</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">Chemistry, CUHK, Hong Kong</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
</div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal"> </div><div style="font:12px/normal Helvetica;margin:0px;font-size-adjust:none;font-stretch:normal">
</div></div></div></div> </div> </div></div><div class="im HOEnZb">
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