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<p>Dear Jiwoo Lee,</p>
<p>From the plot it seems that your calculation contains many more
Wannier charge centers than the reference example. Since the
number of WCC corresponds to the number of bands considered by
Wannier90, it seems likely that you need to change the
"exclude_bands" input in the Wannier90 input file to only consider
the 10 lowest bands.</p>
<p>A common cause for this issue is that VASP will automatically
increase the number of bands if the initially specified number
does not fit the number of cores. For example, if you run this
calculation on a 32-core machine you might obtain 32 bands instead
of the 15 specified in the NBANDS variable of the INCAR file. To
adjust for that, you would have to then change the "exclude_bands"
tag to "11-32" (instead of "11-15").</p>
<p>I hope this solves your problem, please don't hesitate to contact
me again if it does not.<br>
</p>
<p>Best regards,</p>
<p>Dominik Gresch<br>
</p>
<div class="moz-cite-prefix">On 28.01.19 08:18, 이지우 wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAOQvy4G3MweiEa+NBj43Ki1KfhyfH0Ao=aCNHY+woKS6zyr4qg@mail.gmail.com">
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<div dir="ltr">Dear developers,
<div><br>
</div>
<div>Hello.</div>
<div><br>
</div>
<div>I am now trying to get a z2-invariant using VASP code but</div>
<div>I've got some problems in plotting the WCC using the
Z2pack.</div>
<div>
<div><br>
</div>
<div>Firstly, I prepared the converged CHGCAR in advance and</div>
<div>got WCC using the z2-implemented VASP code.</div>
<div><br>
</div>
<div>The material is Bi bulk structure.</div>
<div>And this is what I got.</div>
<div><br>
</div>
<div><img src="cid:part1.49D57771.CA94A2CE@phys.ethz.ch"
alt="image.png" class="gmail-CToWUd gmail-a6T"
tabindex="0" height="307" width="535"><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>And this is the result provided in z2pack GitHub.</div>
<div><br>
</div>
<div><img src="cid:part2.27AEF4A8.B9FA1D85@phys.ethz.ch"
alt="image.png" class="gmail-CToWUd gmail-a6T"
tabindex="0" height="316" width="536"><br>
</div>
<div><br>
</div>
<div>The main problem is where i made <font color="#ff0000">highlight
with red circles</font>.</div>
<div>There are some condensed horizontal points that also
middle point of largest gap (blue diamonds) are changed.</div>
<div>In addition, the points near the two extreme x-axis
ends are increased.</div>
<div>Except for those, other points look very similar with
z2pack provided result.</div>
<div><br>
</div>
<div>I've tested few options,</div>
<div>
<ul>
<li style="margin-left:15px">pos_tol<br>
</li>
<li style="margin-left:15px">move_tol<br>
</li>
<li style="margin-left:15px">gap_tol<br>
</li>
<li style="margin-left:15px">num_lines<br>
</li>
<li style="margin-left:15px">min_neighbour_dist<br>
</li>
</ul>
</div>
<div>however, they doesn't remove the condensed horizontal
points.</div>
<div><br>
</div>
<div>Are there any ways/solutions that I can make a try?</div>
<div><br>
</div>
<div>------------------------------------------------------------------------------------</div>
<div>This the "run.py" I have used.</div>
<div><br>
</div>
<div>
<div>#!/home/woosun/Programs/Python3/bin/python3</div>
<div>import os</div>
<div>import matplotlib</div>
<div>matplotlib.use('Agg')</div>
<div>import matplotlib.pyplot as plt</div>
<div>import z2pack</div>
<div><br>
</div>
<div># Creating the System. Note that the SCF charge file
does not need to be</div>
<div># copied, but instead can be referenced in the .files
file.</div>
<div># The k-points input is appended to the .in file</div>
<div># The command (mpirun ...) will have to be replaced
to match your system.</div>
<div>system = z2pack.fp.System(</div>
<div> input_files=["input/CHGCAR", "input/INCAR",
"input/POSCAR", "input/POTCAR", "input/wannier90.win" ],</div>
<div> kpt_fct=z2pack.fp.kpoint.vasp,</div>
<div> kpt_path="KPOINTS",</div>
<div> command="mpirun
/home/woosun/Source_codes/vasp544/vasp.5.4.4_for_z2/bin/vasp_ncl
> stdout"</div>
<div>)</div>
<div><br>
</div>
<div>if not os.path.exists('./results'):</div>
<div> os.mkdir('./results')</div>
<div>if not os.path.exists('./plots'):</div>
<div> os.mkdir('./plots')</div>
<div><br>
</div>
<div># Running the WCC calculation - standard settings</div>
<div>result_0 = z2pack.surface.run(</div>
<div> system=system,</div>
<div> surface=lambda s, t: [0, s / 2, t],</div>
<div> save_file = './results/res_0.p',</div>
<div> load=True</div>
<div>)</div>
<div>result_1 = z2pack.surface.run(</div>
<div> system=system,</div>
<div> surface=lambda s, t: [0.5, s / 2, t],</div>
<div> save_file = './results/res_1.p',</div>
<div> load=True</div>
<div>)</div>
<div><br>
</div>
<div># Plotting WCC evolution</div>
<div>fig, ax = plt.subplots(1, 2, sharey=True, figsize =
(9,5))</div>
<div><br>
</div>
<div>z2pack.plot.wcc(result_0, axis=ax[0])</div>
<div>z2pack.plot.wcc(result_1, axis=ax[1])</div>
<div>plt.savefig('plots/plot.pdf', bbox_inches = 'tight')</div>
<div><br>
</div>
<div>print('Z2 topological invariant at kx = 0:
{0}'.format(z2pack.invariant.z2(result_0)))</div>
<div>print('Z2 topological invariant at kx = 0.5:
{0}'.format(z2pack.invariant.z2(result_1)))</div>
</div>
<div><br>
</div>
<div>------------------------------------------------------------------------------------<br>
</div>
<div><br>
</div>
<div>Thank you so much for reading the long email.</div>
<div><br>
</div>
<div>I will look forward to having your reply. :)</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Jiwoo Lee.</div>
</div>
<div><br>
</div>
-- <br>
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<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;padding:0px;margin:0px;border:0px;line-height:17.3333320617676px"><span
style="line-height:normal"><font
size="2"><b>JIWOO LEE</b></font></span><span
style="font-size:14px;font-family:Gulim;line-height:normal"> | </span><span
style="font-size:10pt;line-height:normal">Research Associate</span></div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><span
style="font-size:10pt">Materials
Theory Group | Department of Materials
Science & Engineering</span><br>
<span style="font-size:10pt">연세대학교
신소재공학과 재료 이론 연구실</span></div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px"><span
style="font-size:10pt">통합과정 이지우</span></div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px"><br>
<span style="font-size:10pt"><b>YONSEI
UNIVERSITY</b></span><br>
<span style="font-size:10pt">50
Yonsei-Ro | Seodaemun-Gu | 120-749 |
Seoul | KOREA </span><br>
<span style="font-size:10pt"><b>M</b> +82-10-7282-5106
| <b>E</b> <a
href="mailto:jiwoo2231@yonsei.ac.kr"
target="_blank"
moz-do-not-send="true">jiwoo2231@yonsei.ac.kr</a> | <b>W</b> </span><a
href="http://www.materials-theory.org/"
style="color:blue;font-family:굴림;font-size:13.3333px"
target="_blank" moz-do-not-send="true">http://www.materials-theory.org/</a></div>
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