<div dir="ltr"><font face="georgia, serif" size="4">Hi, Krack </font><div><font face="georgia, serif" size="4">Thanks for your patience ! </font></div><div><font size="4"><font face="georgia, serif" style="">How should I use more cores to </font>accelerate the calculation in cp2k inputfile ? Should I add some more statement ?<font face="georgia, serif" style=""><br></font></font><br>在 2018年9月14日星期五 UTC+8下午3:27:21，Matthias Krack写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">As reported in the CP2K output headers</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">GLOBAL| Total number of message passing processes <wbr> 1</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">GLOBAL| Number of threads for this process <wbr> 36</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">both runs were not MPI parallel and only OpenMP parallel using the same resources, i.e. one MPI process and 36 OpenMP
threads. Thus it is not surprising that you observed no acceleration, since you used the same resources. Moreover, the use of more than 8 threads per (MPI) process is rarely beneficial for CP2K runs and will result rather in a slowdown than a speedup. You
have to launch the runs properly, e.g. using something like “mpiexec –n 12 cp2k.popt” which depends, of course, on your installation. If you are using a cp2k.psmp executable, then you should set in addition “export OMP_NUM_THREADS=1”.</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Matthias</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1f497d">
</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <a href="javascript:" target="_blank" gdf-obfuscated-mailto="ulHSLoq3BgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="ulHSLoq3BgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>>
<b>On Behalf Of </b>Tianshu Jiang in Beijing<br>
<b>Sent:</b> Freitag, 14. September 2018 03:50<br>
<b>To:</b> cp2k <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="ulHSLoq3BgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>><br>
<b>Subject:</b> [CP2K:10729] Re: How to accelerate the calculation of pdos ?</span></p>
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<p class="MsoNormal">Hi Krack, thanks for your reply.</p>
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<p class="MsoNormal">In the attachment, bilayerIso.out is the file output by 1 core and bilayerIsoPara.out is the file output by 12cores. </p>
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<p class="MsoNormal">I have no idea where the problem is. <br>
<br>
<span style="font-family:"MS Gothic"">在</span> 2018<span style="font-family:"MS Gothic"">年</span>9<span style="font-family:"MS Gothic"">月</span>12<span style="font-family:"MS Gothic"">日星期三</span> UTC+8<span style="font-family:"MS Gothic"">下午</span>7:58:50<span style="font-family:"MS Gothic"">，</span>Matthias
Krack<span style="font-family:"MS Gothic"">写道：</span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt">Hi Tianshu Jiang<br>
<br>
without providing the CP2K output files of your 1-core and 12-cores runs, it is quite unlikely that you will get any reasonable hint from someone in this forum.<br>
<br>
Matthias</span><br>
<br>
On Wednesday, 12 September 2018 04:41:07 UTC+2, Tianshu Jiang in Beijing wrote:</p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Georgia",serif">Hi everyone in cp2k community,</span></p>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Georgia",serif">I am using cp2k to calculate the pdos of graphene, but the time spent to completing the calculation when I use 1 core and 12 cores is the same.</span></p>
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<p class="MsoNormal"><span style="font-size:18.0pt;font-family:"Georgia",serif">The version I compile is </span><span style="font-size:13.5pt;font-family:"Georgia",serif">Linux-x86-64-gfortran, and I use cp2k.psmp to finish the job. </span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Georgia",serif">But from the *.out file I get that in both situation (1 core and 12 cores), the job finished after half an hour from beginning.</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Georgia",serif">My question is how can I accelerate the calculation using parallel computing ?</span></p>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Georgia",serif">The following is my inputfile. Thanks for your reply !</span></p>
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<div style="border:solid #bbbbbb 1.0pt;padding:0cm 0cm 0cm 0cm;word-wrap:break-word">
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600">&GLOBAL</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> PROJECT trilayerABCIso</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> RUN_TYPE ENERGY </span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> PRINT_LEVEL MEDIUM</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600">&END GLOBAL</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New""> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600">&FORCE_EVAL</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> METHOD Quickstep</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &DFT</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> BASIS_SET_FILE_NAME BASIS_MOLOPT</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> POTENTIAL_FILE_NAME POTENTIAL</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New""> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &POISSON</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> PERIODIC XYZ </span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END POISSON</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &SCF</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> SCF_GUESS ATOMIC</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> EPS_SCF 1.0E-6</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> MAX_SCF 300 </span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New""> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # The following settings help with convergence:</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ADDED_MOS 100 </span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> CHOLESKY INVERSE</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &SMEAR ON</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> METHOD FERMI_DIRAC</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ELECTRONIC_TEMPERATURE [K] 300 </span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END SMEAR</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &DIAGONALIZATION</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ALGORITHM STANDARD</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> EPS_ADAPT 0.01</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END DIAGONALIZATION</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &MIXING</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> METHOD BROYDEN_MIXING</span><span style="font-size:10.0pt;font-family:"Courier New""></span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ALPHA 0.2 </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> BETA 1.5</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> NBROYDEN 8</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END MIXING</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END SCF</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &XC</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &XC_FUNCTIONAL PBE</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END XC_FUNCTIONAL</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END XC</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &PRINT</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &PDOS</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # print all projected DOS available:</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> NLUMO -1</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # split the density by quantum number:</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> COMPONENTS</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &E_DENSITY_CUBE ON</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> STRIDE 1 1 1</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END E_DENSITY_CUBE</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END PRINT</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END DFT</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &SUBSYS</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &CELL</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # create a hexagonal unit cell:</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ABC [angstrom] 2.4612 2.4612 26.72</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ALPHA_BETA_GAMMA 90. 90. 60.</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> SYMMETRY HEXAGONAL</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> PERIODIC XYZ</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # and replicate this cell (see text):</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> MULTIPLE_UNIT_CELL 6 6 1</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END CELL</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &TOPOLOGY</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # also replicate the topology (see text):</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> MULTIPLE_UNIT_CELL 6 6 1</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END TOPOLOGY</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &COORD</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> SCALED</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> # ABC stacked</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 1./3 1./3 0.</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 0. 3./3 0.</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 1./3 1./3 1./8</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 2./3 2./3 1./8</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 2./3 2./3 2./8</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> C 3./3 0. 2./8</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &KIND C</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> ELEMENT C</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> BASIS_SET TZVP-MOLOPT-GTH</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> POTENTIAL GTH-PADE-q4</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END KIND</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> &END SUBSYS</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600">&END FORCE_EVAL</span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Courier New";color:#666600"> </span></p>
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<p class="MsoNormal" style="background:#fafafa"><span style="font-size:10.0pt;font-family:"Georgia",serif"> </span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"> </p>
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<p class="MsoNormal"> </p>
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</div>
</blockquote>
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</blockquote>
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