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<p>Thanks for your help once again. I do not have XCrysDen and I have been having problems installing it. This is weird as with Crystal builder the atoms were well separated and different. One more thing: Where can I find the ccorect coordinates? any idea
how to form the atomic positions?</p>
<p><br>
</p>
<p>Thanks</p>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> pw_forum-bounces@pwscf.org <pw_forum-bounces@pwscf.org> on behalf of Duc-Long NGUYEN <longnguyenqtr@gmail.com><br>
<b>Sent:</b> Monday, January 11, 2016 9:53 PM<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] Atomic positions for Black Phosphorus calculations</font>
<div> </div>
</div>
<div><tt>Hi,</tt><tt><br>
</tt><tt><br>
</tt><tt>You could use xcrysden to check your input.</tt><tt><br>
</tt><tt>This is the result with your input:</tt><tt><br>
</tt><tt>Number of Atoms: 8</tt><tt><br>
</tt><tt>Number of Frames: 12</tt><tt><br>
</tt><tt>WARNING: Atom 1 and atom 3 overlap !!! Atom 3 deleted !!!</tt><tt><br>
</tt><tt>WARNING: Atom 2 and atom 7 overlap !!! Atom 7 deleted !!!</tt><tt><br>
</tt><tt>WARNING: Atom 4 and atom 8 overlap !!! Atom 8 deleted !!!</tt><tt><br>
</tt><tt>WARNING: Atom 5 and atom 6 overlap !!! Atom 6 deleted !!!</tt><tt><br>
</tt><tt>That was also why pwscf showed that error.</tt><tt><br>
</tt><tt><br>
</tt><tt>Duc-Long</tt><tt><br>
</tt><br>
<div class="moz-cite-prefix">On 1/12/2016 7:46 AM, Elio Physics wrote:<br>
</div>
<blockquote type="cite">
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<p>Dear Duc-Long,</p>
<p><br>
</p>
<p>thanks for your response. I do not think they have the same coordinate. The "y" coordinate of one is
<b>0.10168</b> while that of the 2nd is <b>1.10168, </b> that is a difference of 1 ang.</p>
<p><br>
</p>
<p>Elio</p>
<br>
<br>
<div style="color:rgb(0,0,0)">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:pw_forum-bounces@pwscf.org"><pw_forum-bounces@pwscf.org></a> on behalf of Duc-Long NGUYEN
<a class="moz-txt-link-rfc2396E" href="mailto:longnguyenqtr@gmail.com"><longnguyenqtr@gmail.com></a><br>
<b>Sent:</b> Monday, January 11, 2016 9:38 PM<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] Atomic positions for Black Phosphorus calculations</font>
<div> </div>
</div>
<div><tt>Dear Elio,</tt><tt><br>
</tt><tt><br>
</tt>
<div><tt>ATOMIC_POSITIONS crystal</tt></div>
<div><tt>P -0.89832 0.89832 0.91944</tt></div>
<div><tt>P -0.39832 0.39832 0.58056</tt></div>
<div><tt><font color="#cc0000"><u>P -0.10168 0.10168 0.08056</u></font></tt></div>
<div><tt>P 0.10168 0.89832 0.91944</tt></div>
<div><tt><font color="#cc0000"><u>P -0.10168 1.10168 0.08056</u></font></tt></div>
<div><tt>P -0.60168 0.60168 0.41944</tt></div>
<div><tt>P -0.39832 1.39832 0.58056</tt></div>
<div><tt>P 0.39832 0.60168 0.41944</tt></div>
<tt>These two atom positions have the same coordinate. This could be the problem</tt><tt>.<br>
</tt><tt><br>
</tt><tt>Duc-Long</tt><br>
<br>
<div class="moz-cite-prefix">On 1/12/2016 6:44 AM, Elio Physics wrote:<br>
</div>
<blockquote type="cite">
<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear all,</p>
<p><br>
</p>
<p>I am trying to perform some calculations on Black Phosphorus (BP). To get the atomic positions I used the Crystal Builder, where I have chosen the lattice type to be base centered orthorhombic. The "builder" produced a set of cartesian and fractional (in
terms of the primitive cell vectors) . I have used the fractional ones and I have also used ibrav=0 with the CELL_PARAMETERS defined as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I have got the following error:</p>
<p><br>
</p>
<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div> from check_atoms : error # 1</div>
<div> atoms # 1 and # 4 overlap!</div>
<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div><br>
</div>
Doing the same calculation with ibrav=8 and using the coordinates produced by the Crystal builder for a simple orthorhombic does not produce any errors. Can anyone please tell me what is wrong with atoms (1) and (4). Is BP simple or base centered orthorhombic..Where
can I find the coorect atomic position of bulk BP? The scf input is below:
<p><br>
</p>
<p> </p>
<div>&CONTROL</div>
<div> prefix='bp',</div>
<div> calculation='scf',</div>
<div> restart_mode='from_scratch',</div>
<div> wf_collect=.true.,</div>
<div> forc_conv_thr=1.D-4</div>
<div> etot_conv_thr=1.D-5</div>
<div> tstress=.true.,</div>
<div> tprnfor=.true.,</div>
<div> pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo',</div>
<div> outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT'</div>
<div> /</div>
<div> &SYSTEM</div>
<div> ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, ecutrho=40, occupations='smearing', london=.true., smearing='mp', degauss=0.035,nbnd=32</div>
<div>/</div>
<div> &ELECTRONS</div>
<div> conv_thr=1.D-8,</div>
<div> mixing_beta=0.1</div>
<div>/</div>
<div>&IONS</div>
<div>ion_dynamics='bfgs'</div>
<div>/</div>
<div>&CELL</div>
<div>cell_dynamics='bfgs'</div>
<div>press=0.0</div>
<div>/</div>
<div>ATOMIC_SPECIES</div>
<div>P 30.97376 P.pbe-n-van.UPF</div>
<div>ATOMIC_POSITIONS crystal</div>
<div>P -0.89832 0.89832 0.91944</div>
<div>P -0.39832 0.39832 0.58056</div>
<div>P -0.10168 0.10168 0.08056</div>
<div>P 0.10168 0.89832 0.91944</div>
<div>P -0.10168 1.10168 0.08056</div>
<div>P -0.60168 0.60168 0.41944</div>
<div>P -0.39832 1.39832 0.58056</div>
<div>P 0.39832 0.60168 0.41944</div>
<div><br>
</div>
<div>K_POINTS automatic</div>
<div> 2 2 2 0 0 0</div>
<div><br>
</div>
<div>CELL_PARAMETERS alat</div>
<div>0.5000 -1.58106 0.0000</div>
<div>0.500 1.58106 0.0000</div>
<div>0.0000 0.00000 4.3763</div>
<div><br>
</div>
<div><br>
</div>
<div>thanks</div>
<div><br>
</div>
<div>Elio Arbid</div>
<div>University of Nottingham</div>
<div>UK</div>
</div>
<br>
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<pre class="moz-signature" cols="72">--
Duc-Long Nguyen
Graduate Student, Molecular Science and Technology Program, TIGP
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
Phone +886 979279073</pre>
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