<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;font-size:14pt"><div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Arial;color:#232323;">Dear Prof. Rubel, and Sheikh,<span style="font:19.0px;"> </span></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;"><span style="font:13.0px Arial;"> ></span>it's good to hear that everything worked with the fresh install. I am </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">also interested to trace the origin of your previous problems, but I </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">cannot reproduce the error. If you still have an access to the previous </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">installation and can reproduce both correct and incorrect results, try </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">to switch packages one-by-one, e.g. replace only BerryPI and see whether </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">it makes a difference. Then do the same with W2W, WIEN2K. This way you </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">can narrow down the reason.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:15.0px Helvetica;color:#232323;">In
order to trace the problem, we tried to reproduce the error. To this
end, we installed different versions of WIEN2WANNIER and BERRYPI.
Eventually, we could find the source of the problem. It originated from
WIEN2WANNIER. As Sheikh said, I changed the w2w script. It worked and
we could get good result. But, we still do not know what is the role of
"*" in <span style="color:#501050;">tmp="$(grep "lapw1 *-c" "$SEEDNAME.dayfile")". </span>As
far as I know –c flag is necessary when inversion symmetry is break
down and complex calculations are needed to be performed by the WIEN2k
code. I am not aware about "*-c" flag. </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;"><span style="font:19.0px;">></span>As far as I know, there is an internal relaxation in GaN wurtzite, which </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">leads to slightly different Ga-N bond lengths (in c-direction and </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">off-axis). Maybe the spontaneous polarization (Ps) is referred to a </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">difference in polarization between two structures with relaxed and </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">unrelaxed internal degrees of freedom? But I do not know for sure. How </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px;color:#232323;">big is the value of Ps reported in the literature?</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">We
are also not sure whether it is referred to the relaxed and unrelaxed
structures. Thus, we tried to check it out. To do this, we selected the
unrelaxed structure for lambda1and the relaxed one for lambda0. Our
result is as follows:</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">3.16596720935 - 3.17586420101 = -0.00989699166 </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">But,
this result is far from reported value in the literature, i.e., SP was
reported to be -0.02 [PRB86, 081302(R) and PRB56, R10024].</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Arial;color:#232323;"> </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;">> In any case, I would think what is the *measurable* quantity related to </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;">change of polarization in GaN and try to calculate that.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:19.0px;color:#232323;min-height:23.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">Does
this mean that one has to try by changing the displacement reproduce
the experimental value? In this case our result depends on the
displacement. Can it be (in this case) an ab initio prediction?</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"> </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">Any comments or idea will be appreciated.<span style="font:19.0px;"> </span></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;">> We suspected that BerryPI may not be compatible with earlier versions of </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;">numpy (before 1.6.2), but I don't think we actually tested it against </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;">numpy
1.4.1. The is the reason why init.sh is so picky. If you confirm that
it works for you with numpy 1.4.1, we can loosen this requirement.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px Helvetica;color:#232323;min-height:19.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px Helvetica;color:#232323;">Yes, NUMPY 1.4.1 works as fine as NUMPY 1.6.2.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:13.0px Courier;color:#232323;min-height:16.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Arial;color:#232323;"><span style="font:18.0px Arial;">> </span>Also
regarding the Numpy version, We actually haven't tested BerryPI any
Numpy older than v1.6.2. This is why the init.sh tries to ignore the
older versions.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:18.0px Arial;color:#232323;">NUMPY
1.4.1 is not an old version of NUMPY. Indeed, NUMPY 1.1.4 is the
latest version of NUMPY that Fedora Core 14 automatically due to its
repository install by yum command. NUMPY 1.6.2 is installed by yum in
Fedora 17.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Arial;color:#232323;"><span style="font:16.0px;">></span><span style="font:18.0px Arial;"> ></span>Another
source of error could be from the older version of BerryPI which was
using a different phase wrapping method. That was causing some issues to
bring the phases between 0 to 2*pi or -pi to +pi range when some of the
phases were close to 0 (may be positive or negative). The method was
completely ignoring those smaller values instead of unwarpping all the
phases to same range. As a result, you would have phase values like
1.999*pi 1.99996*pi 1.9994*pi <span style="text-decoration:underline;">-0.0001*pi</span> instead of 1.999*pi 1.99996*pi 1.9994*pi <span style="text-decoration:underline;">1.9999*pi.</span> This would have messed up your average phase value and polarization.</div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">We
are still working on the above comment, but we are not sure whether we
understand it completely. Clarification will help to do it. </div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;min-height:18.0px;"><br></div>
<div style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">Thank for your cooperation.</div>
<div dir="ltr" style="margin:0.0px 0.0px 0.0px 0.0px;font:16.0px;color:#232323;">SH. Rahimi</div></div></body></html>