<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px"><div id="yiv9596471843"><div class="qtdSeparateBR"><br><br></div><div class="yiv9596471843yqt9328499114" id="yiv9596471843yqtfd66332"><div id="yui_3_16_0_1_1463657997687_3316"><div id="yui_3_16_0_1_1463657997687_3315" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_2921"><span></span></div><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3117" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"><br><div class="yiv9596471843y_msg_container" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3116"><div id="yiv9596471843"><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3115"><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3114" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"><div id="yiv9596471843yui_3_16_0_1_1463641816366_3006"><span></span></div> <div id="yui_3_16_0_1_1463657997687_3439" class="yiv9596471843qtdSeparateBR"><br clear="none"><div id="yui_3_16_0_1_1463657997687_3740" dir="ltr">Hello wannier90 list,</div><div id="yui_3_16_0_1_1463657997687_3762" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3830" dir="ltr">I have found the root of the problem. <br></div><div id="yui_3_16_0_1_1463657997687_3831" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3832" dir="ltr">My structure was a snapshot of an MD run. In the INCAR I had <br></div><div id="yui_3_16_0_1_1463657997687_3887" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3888" dir="ltr">POTIM = 2.0</div><div id="yui_3_16_0_1_1463657997687_3889" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3890" dir="ltr">I had also explicitly set the calculation to be static with:</div><div id="yui_3_16_0_1_1463657997687_3894" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3929" dir="ltr">NSW = 0 (Max ionic steps)<br id="yui_3_16_0_1_1463657997687_3906">IBRION = -1 <br></div><div id="yui_3_16_0_1_1463657997687_3895" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3973" dir="ltr">Despite this static setting, for some reason leaving the POTIM flag set caused the issue. Removing it solves the problem.</div><div id="yui_3_16_0_1_1463657997687_3974" dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_3975" dir="ltr">Thanks, <br></div><div dir="ltr">Conn</div><div dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_4028" dir="ltr">---------------</div><div id="yui_3_16_0_1_1463657997687_4029" dir="ltr">Department of Chemistry<br></div><div id="yui_3_16_0_1_1463657997687_4030" dir="ltr">University of Bath<br></div><div dir="ltr"><br></div><div id="yui_3_16_0_1_1463657997687_4031" dir="ltr"><br></div></div><div class="yiv9596471843yqt5561797201" id="yiv9596471843yqt68367"></div></div></div></div><br clear="none"><br clear="none"></div> </div><div id="yui_3_16_0_1_1463657997687_3438" class="yiv9596471843qtdSeparateBR"><br clear="none"><br clear="none"></div><div class="yiv9596471843yahoo_quoted" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3119" style="display:block;"><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3118" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"> </div> </div></div></div></div></div><div class=".yiv9596471843yahoo_quoted"> <div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3836" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"> <div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3835" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:16px;"> <div dir="ltr"><font size="2" face="Arial"> On Thursday, 19 May 2016, 7:55, Giovanni Pizzi <giovanni.pizzi@epfl.ch> wrote:<br clear="none"></font></div> <br clear="none"><br clear="none"> <div class="yiv9596471843y_msg_container" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3834"><div id="yiv9596471843"><div id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3833">
Hi,
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3838">I’m not sure of how the VASP interface works, but is it possible that you are relaxing the cell, and VASP (correctly, I guess) passes to Wannier90 the output (=relaxed) coordinates?</div>
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3840">Also, it is strongly suggested to sign your posts with your affiliation.</div>
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<div class="yiv9596471843">Best,</div>
<div class="yiv9596471843">Giovanni</div>
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Giovanni Pizzi</div>
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Theory and Simulation of Materials and MARVEL, EPFL</div>
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<blockquote class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3844" type="cite">
<div class="yiv9596471843yqt8695741926" id="yiv9596471843yqt22754"><div class="yiv9596471843">On 18 May 2016, at 23:45, Conn ORourke <<a rel="nofollow" shape="rect" class="yiv9596471843" ymailto="mailto:conn.orourke@yahoo.co.uk" target="_blank" href="mailto:conn.orourke@yahoo.co.uk">conn.orourke@yahoo.co.uk</a>> wrote:</div>
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463643721966_3841" style="background-color:rgb(255, 255, 255);font-family:HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;">
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5724" style="background-color:rgb(255, 255, 255);font-family:HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;">
<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_2820">Hi there, <br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4520"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4519">I was wondering if anyone could explain a problem I am seeing with the wannier90 library compiled in VASP.</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4484"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4485">The problem is that the Cartesian coords in the seedname.win file generated by the library are different to that of the original POSCAR. Likewise the bond lengths from the wannier90_centres.xyz
file are different to that of the POSCAR file.<br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4559"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4560">For example:</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4561">
<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5734"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4562">For a POSCAR file with the following lattice:</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5735"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4563"><i class="yiv9596471843"><b class="yiv9596471843">15.932414 0.0000000 0.00000000<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5739" clear="none">
0.0000000 16.005113 0.00000000<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5740" clear="none">
</b></i>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5854"><i class="yiv9596471843"><b class="yiv9596471843"> 0.0000000 0.0000000 15.9324110</b></i></div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5855"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5856">with the two first atoms:<br class="yiv9596471843" clear="none">
</div>
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5857"><i class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6166"><b class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6165">Direct<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4572" clear="none">
0.1665762551037838 0.2052544038323533 0.1664989385925252<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4573" clear="none">
0.1796712991481728 0.1930070499806985 0.6768832070032641</b></i><br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_4574" clear="none">
<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5858"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5859">and equivalent Cartesian coords:</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5860"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5867"><i class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6155"><b class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6154"> 2.653962 3.285120 2.652730<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5874" clear="none">
2.862597 3.089100 10.784382</b></i></div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5962"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5963">the wannier90.win file produced has:</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5964"><i class="yiv9596471843"><b class="yiv9596471843"><br class="yiv9596471843" clear="none">
</b></i></div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5965"><i class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6146"><b class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6145">begin unit_cell_cart<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5984" clear="none">
15.9324140 0.0000000 0.0000000<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5985" clear="none">
0.0000000 16.0051130 0.0000000<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5986" clear="none">
0.0000000 0.0000000 15.9324110<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5987" clear="none">
end unit_cell_cart<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5988" clear="none">
<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5989" clear="none">
begin atoms_cart<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5990" clear="none">
Mg 2.6899086 3.2554542 2.6535155<br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5991" clear="none">
Mg 2.8794998 3.0745452 10.7780014</b></i><br class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_5992" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6004"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6067">If I generate the wannier90.win file by hand, and explicitly enter the correct Cartesian positions of the atoms into the atoms_cart block, those in the wannier90.wout file are again different.
I also noticed that in the output file it says:</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6097"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6098"><b class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6127"><i class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6123"> Ignoring <atoms_cart> in input file</i></b></div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6229"><br class="yiv9596471843" clear="none">
</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6242">Is there some reason why the atoms_cart block doesn't get read, or a flag to set the code to read it.<br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6068"><br class="yiv9596471843" clear="none">
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</div>
<div class="yiv9596471843" dir="ltr" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6357">
<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6356">Are these problems as a result of the compilation, or something else?</div>
<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6358"><br class="yiv9596471843" clear="none">
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<div class="yiv9596471843" id="yiv9596471843yui_3_16_0_ym19_1_1463606983494_6359">Many thanks!<br class="yiv9596471843" clear="none">
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