<div dir="ltr"><div>Dear Aron,<br><br></div>thanks for your kind reply. <br>Still look forward to receiving any help on the error from other users.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 29, 2015 at 1:22 PM, Aron Szabo <span dir="ltr"><<a href="mailto:szaboa@iis.ee.ethz.ch" target="_blank">szaboa@iis.ee.ethz.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Dear Seyed,<br>
<br>
I've managed to get nicely converged Wannier functions for
phosphorene by using sp3 projections on each 4 atoms, therefore
including 6 conduction bands in the calculation too with the
disentanglement method. The largest spread was 2 A^2. In my
experience it should not be much larger than 3 A^2 for most
semiconductors. And the imaginary part of the Hamiltonian should
be practically 0 everywhere (or in the order of magnitude of
1e-6). I was using 21x21x1 k points. I did not check with an even
mesh, but sometimes it matters a lot for the wannierization
whether you use even or odd mesh. I've used VASP, and I'm not an
expert with espresso, and I did not look into you input and output
files. Just wanted share my experience with phosphorene.<br>
<br>
Best,<br>
Aron<div><div class="h5"><br>
<br>
On 06/29/2015 09:38 AM, Seyed Mojtaba Rezaei Sani wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>
<div>
<div>
<div>Dear Nicola,<br>
<br>
</div>
Thanks. Phosphorene has four P atoms in its unit cell so
considering 10 valence bands and therefore 10 WFs, we
can't fit a projection of s orbital on every atom and bond
to this number. <br>
</div>
But I have found new thing. Instead of increasing the number
of kpoints in wannier input, I chose a coarser grid which
seems to be fine enough to provide converged WFs with both
versions of codes. The resulted band structure completely
matches the PWscf one but there is an error in transport
section implies that there are 0 unit cells and Wfs inside
the principal layer:<br>
<br>
*---------------------------------------------------------------------------*<br>
|
TRANSPORT |<br>
*---------------------------------------------------------------------------*<br>
<br>
<br>
Calculation of Quantum Conductance and DoS: bulk mode<br>
<br>
Maximum imaginary part of the real-space Hamiltonian:
0.189159<br>
<br>
------------------------------------------------------------------------------<br>
Maximum real part of the real-space Hamiltonian at each
lattice point<br>
--------------------------------------------------------------<br>
Lattice point R Max |H_ij(R)|<br>
-1 0.000000<br>
0 7.773991<br>
1 0.000000<br>
--------------------------------------------------------------<br>
<br>
Number of unit cells inside the principal layer: 0<br>
Number of Wannier Functions inside the principal layer:
0<br>
<br>
Calculating quantum conductance and density of states...<br>
ERROR: IN ZGESV IN tran_transfer, INFO= -4<br>
Exiting.......<br>
tran_transfer: problem in ZGESV 1<br>
<br>
</div>
<br>
<br>
in/output files are attached. Any help would be greatly
appreciated.<br>
</div>
I have a stupid question too, What are the satisfying values for
the imaginary part and spread of WFs?<br>
<br>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jun 25, 2015 at 11:47 PM,
Nicola Marzari <span dir="ltr"><<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
Dear Seyed,<br>
<br>
<br>
any news on this?<span><font color="#888888"><br>
<br>
nicola</font></span>
<div>
<div><br>
<br>
<br>
<br>
On 15/06/2015 14:17, Nicola Marzari wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks.<br>
<br>
At first sight the two espresso codes give the same
eigenvalues in the<br>
nscf,<br>
but being run with two different parallelization
choices, the<br>
phases of the wannier functions will all be different,
so<br>
it's like dealing with two independent calculations.
So the question is<br>
for Wannier - to see if you have converged to the
correct localized state,<br>
or not. Usually, if the projections are correct, it
shouldn't matter, but<br>
maybe in this case they are not correct, and hten the
codes randomly<br>
converges, or not.<br>
<br>
One of the outputs records a large imaginary part -
that's a bad sign.<br>
The other has two much less localized wavefunctions -
maybe good, maybe<br>
bad.<br>
<br>
Can you try with projections that have a s orbital at
every atom, and<br>
a s orbital at every bond? Those should work, and it
would be nice<br>
to see that both codes give the same results.<br>
<br>
Otherwise, we'll need to dig deeper.<br>
<br>
nicola<br>
<br>
<br>
<br>
<br>
On 15/06/2015 13:41, Seyed Mojtaba Rezaei Sani wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Nicola<br>
<br>
Thanks a lot for your kind response. Surely I did
checked outputs before<br>
too. There was no considerable difference between
them and also there is<br>
no unconverged band message. So I can say:<br>
<br>
Re 1) Every thing works perfectly both in 5.1 and
5.1.2 versions except<br>
the disappointing obtained wannier90 band structure
by the later.<br>
Re 2) No difference.<br>
<br>
As more details, please find all in/output files for
both versions<br>
(except UNK ones which are too big) here:<br>
<br>
<a href="https://www.dropbox.com/sh/xhd3etb6zfz2e7c/AAClTpe-aGkwXVrzDcIq6L7Aa?dl=0" rel="noreferrer" target="_blank">https://www.dropbox.com/sh/xhd3etb6zfz2e7c/AAClTpe-aGkwXVrzDcIq6L7Aa?dl=0</a><br>
<br>
Thanks again,<br>
<br>
On Mon, Jun 15, 2015 at 12:23 PM, Nicola Marzari
<<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a><br>
<mailto:<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>>>
wrote:<br>
<br>
<br>
<br>
Hi Sani,<br>
<br>
<br>
I had mentioned in my email that you should
check both<br>
your input and your output files - since the
problems seem due<br>
to the change in version of quantum-espresso (I
do appreciate you<br>
did check your input files, but I do wonder why
you didn't<br>
read the email in full, since it was asking
about the output).<br>
<br>
So - do you see any difference in the output
files of quantum<br>
espresso?<br>
<br>
From your plots my first guess would be that
you have some states<br>
that<br>
are not converged at some k-point.<br>
<br>
1) can you confirm that in an older version of
QE everything<br>
worked perfectly (*which one*?, and in 5.1.2 you
have the problems<br>
below?<br>
<br>
2) do the outputs in the two cases differ - for
the QE runs, and<br>
for the<br>
wannier runs, when run with *identical* inputs?
If so, in what do<br>
they differ.<br>
<br>
Let us know re 1) and 2) - thanks a lot,<br>
<br>
nicola<br>
<br>
<br>
<br>
On 15/06/2015 09:40, Seyed Mojtaba Rezaei Sani
wrote:<br>
<br>
Dear all<br>
<br>
I am looking forward to receive any kind
help.<br>
<br>
On Wed, Jun 10, 2015 at 2:59 PM, Seyed
Mojtaba Rezaei Sani<br>
<<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>><br>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a><br>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>>>>
wrote:<br>
<br>
Dear Prof. Marzari<br>
<br>
As you suggested I checked input files
and they were exactly<br>
identical. but the difference in result
remains.<br>
I tried to make a change in
calculations so I increased<br>
number of<br>
kpoints in non scf and wannier
calculations from<br>
a mesh of 12*12*1 to 16*16*1. The
result was an improvement<br>
in band<br>
structure. you can find the plot
attached. But<br>
there are still some inadequacies to
the pw band in the<br>
region gamma<br>
to X.<br>
Again I increased the grid to a 24*24*1
mesh which<br>
encountered this<br>
error:<br>
<br>
Unable to satisfy B1 with any of the
first 12 shells<br>
Your cell might be very long, or you
may have an<br>
irregular MP grid<br>
Try increasing the parameter
search_shells in the win<br>
file (default=12)<br>
<br>
Setting the parameter search_shells =
60 solved the problem<br>
but now<br>
inadequacies are in the region S to Y
(the plot is<br>
attached).<br>
I don't know if there is any parameter
that I could change<br>
to solve<br>
this problem. Please give me any
probable hint.<br>
Thanks,<br>
<br>
On Wed, Jun 10, 2015 at 2:53 PM, Seyed
Mojtaba Rezaei Sani<br>
<<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>><br>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a><br>
<mailto:<a href="mailto:s.m.rezaeisani@gmail.com" target="_blank">s.m.rezaeisani@gmail.com</a>>>>
wrote:<br>
<br>
Dear Prof. Marzari<br>
<br>
As you suggested I checked input
files and they were<br>
exactly<br>
identical. but the difference in
result remains.<br>
I tried to make a change in
calculations so I increased<br>
number<br>
of kpoints in non scf and wannier
calculations from<br>
a mesh of 12*12*1 to 16*16*1. The
result was an<br>
improvement in<br>
band structure. you can find the
plot attached. But<br>
there are still some inadequacies
to the pw band in the<br>
region<br>
gamma to X.<br>
Again I increased the grid to a
24*24*1 mesh which<br>
encountered<br>
this error:<br>
<br>
Unable to satisfy B1 with any of
the first 12 shells<br>
Your cell might be very long, or
you may have an<br>
irregular MP grid<br>
Try increasing the parameter
search_shells in the win<br>
file (default=12)<br>
<br>
Setting the parameter search_shells
= 60 solved the<br>
problem but<br>
now inadequacies are in the region
S to Y (the plot is<br>
attached).<br>
I don't know if there is any
parameter that I could<br>
change to<br>
solve this problem. Please give me
any probable hint.<br>
Thanks,<br>
<br>
On Thu, May 28, 2015 at 12:39 PM,
Nicola Marzari<br>
<<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>
<mailto:<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>><br>
<mailto:<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>
<mailto:<a href="mailto:nicola.marzari@epfl.ch" target="_blank">nicola.marzari@epfl.ch</a>>>><br>
wrote:<br>
<br>
<br>
<br>
Well, the obvious thing to do
is making sure your<br>
inputs are exactly identical,
you re-run the<br>
calculations<br>
to make sure the error shows up
again, and then you<br>
start<br>
doing a diff in the output
files of<br>
quantum-espresso, and<br>
see where there is a
difference.<br>
<br>
nicola<br>
<br>
<br>
<br>
<br>
On 28/05/2015 09:07, Seyed
Mojtaba Rezaei Sani<br>
wrote:<br>
<br>
Dear Wannier90 users,<br>
<br>
I am trying to calculate
wannier functions for<br>
phosphorene using<br>
wannier90. first I tried to
plot band structure<br>
using both<br>
quantum-espresso and
wannier90. Results were in<br>
good<br>
agreement. Now I<br>
have upgraded espresso to
5.1.2 version but<br>
with the<br>
same inputs the<br>
obtained results are not
similar.<br>
All files are attached and
here in .win input:<br>
<br>
num_bands = 10<br>
num_wann = 10<br>
num_iter = 500<br>
<br>
Begin Unit_Cell_Cart<br>
Bohr<br>
6.282237122
0.000000000<br>
0.0000000000<br>
0.000000000
8.651074073<br>
0.0000000000<br>
0.000000000
0.000000000<br>
26.456165734<br>
End Unit_Cell_Cart<br>
<br>
Begin Atoms_Frac<br>
P1 0.010000000
0.086656382<br>
0.152592466<br>
P1 0.010000000
0.913343530<br>
0.001000000<br>
P2 0.510000000
0.413343618<br>
0.152592466<br>
P2 0.510000000
0.586656470<br>
0.001000000<br>
End Atoms_Frac<br>
<br>
Begin Projections<br>
P1:sp3<br>
P2:py<br>
End Projections<br>
<br>
bands_plot = true<br>
<br>
begin kpoint_path<br>
G 0.0000 0.0000 0.0000 X
0.5000 0.0000 0.0000<br>
x 0.5000 0.0000 0.0000 S
0.5000 0.5000 0.0000<br>
S 0.5000 0.5000 0.0000 Y
0.0000 0.5000 0.0000<br>
Y 0.0000 0.5000 0.0000 G
0.0000 0.0000 0.0000<br>
end kpoint_path<br>
<br>
mp_grid = 12 12 1<br>
<br>
begin kpoints<br>
0.00000000 0.00000000
0.00000000<br>
.<br>
.<br>
.<br>
0.91666667 0.91666667
0.00000000<br>
End Kpoints<br>
<br>
I would greatly appreciate
it if you kindly<br>
give me some<br>
hints.<br>
<br>
Best regards,<br>
<br>
--<br>
Seyed Mojtaba Rezaei Sani<br>
<br>
Institute for Research in
Fundamental Sciences<br>
(IPM)<br>
School of Nano-Science<br>
Shahid Farbin Alley<br>
Shahid Lavasani st<br>
P.O. Box 19395-5531<br>
Tehran, Iran<br>
Tel: +98 21 2310 (3069)<br>
<br>
<br>
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<br>
<br>
--<br>
<br>
<br>
<br>
----------------------------------------------------------------------<br>
Prof Nicola Marzari, Chair of
Theory and<br>
Simulation of<br>
Materials, EPFL<br>
Director, National Centre for
Competence in<br>
Research NCCR<br>
MARVEL, EPFL<br>
<br>
<br>
<br>
<br>
--<br>
Seyed Mojtaba Rezaei Sani<br>
<br>
Institute for Research in
Fundamental Sciences (IPM)<br>
School of Nano-Science<br>
Shahid Farbin Alley<br>
Shahid Lavasani st<br>
P.O. Box 19395-5531<br>
Tehran, Iran<br>
Tel: +98 21 2310 (3069)<br>
<br>
<br>
<br>
<br>
--<br>
Seyed Mojtaba Rezaei Sani<br>
<br>
Institute for Research in Fundamental
Sciences (IPM)<br>
School of Nano-Science<br>
Shahid Farbin Alley<br>
Shahid Lavasani st<br>
P.O. Box 19395-5531<br>
Tehran, Iran<br>
Tel: +98 21 2310 (3069)<br>
<br>
<br>
<br>
<br>
--<br>
Seyed Mojtaba Rezaei Sani<br>
<br>
Institute for Research in Fundamental
Sciences (IPM)<br>
School of Nano-Science<br>
Shahid Farbin Alley<br>
Shahid Lavasani st<br>
P.O. Box 19395-5531<br>
Tehran, Iran<br>
Tel: +98 21 2310 (3069)<br>
<br>
<br>
--<br>
<br>
<br>
----------------------------------------------------------------------<br>
Prof Nicola Marzari, Chair of Theory and
Simulation of Materials,<br>
EPFL<br>
Director, National Centre for Competence in
Research NCCR MARVEL,<br>
EPFL<br>
<br>
<br>
<br>
<br>
--<br>
Seyed Mojtaba Rezaei Sani<br>
<br>
Institute for Research in Fundamental Sciences (IPM)<br>
School of Nano-Science<br>
Shahid Farbin Alley<br>
Shahid Lavasani st<br>
P.O. Box 19395-5531<br>
Tehran, Iran<br>
Tel: +98 21 2310 (3069)<br>
</blockquote>
<br>
</blockquote>
<br>
-- <br>
<br>
----------------------------------------------------------------------<br>
Prof Nicola Marzari, Chair of Theory and Simulation of
Materials, EPFL<br>
Director, National Centre for Competence in Research
NCCR MARVEL, EPFL<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div>
<div dir="ltr"><span><font color="#888888"><span style="font-family:arial,helvetica,sans-serif">Seyed
Mojtaba Rezaei Sani<br>
<br>
Institute for Research in Fundamental Sciences (IPM)<br>
School of Nano-Science<br>
<font><span>Shahid Farbin Alley<br>
Shahid Lavasani st</span></font><br>
<font><span><font><span>P.O. Box 19395-5531<br>
</span></font>Tehran, Iran<br>
</span></font>Tel: +98 21 2310 (3069)<br>
</span></font></span></div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre><div><div class="h5">_______________________________________________
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</pre>
</blockquote>
<br>
</div>
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<br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><span><font color="#888888"><span style="font-family:arial,helvetica,sans-serif">Seyed Mojtaba Rezaei Sani<br><br>Institute for Research in Fundamental Sciences (IPM)<br>
School of Nano-Science<br><font><span>Shahid Farbin Alley<br>
Shahid Lavasani st</span></font><br><font><span><font><span>P.O. Box 19395-5531<br></span></font>Tehran, Iran<br></span></font>Tel: +98 21 2310 (3069)<br></span></font></span></div></div>
</div>