Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread catrina desport
To respected siesta users,

when I run input using ./input  SysLabel.EPSIMG and then I write ./optical 
without the arrow, still the segmentation fault occurs ?!?! What is the reason?

Regards,
Catrina





From: Marty Blaber [EMAIL PROTECTED]
To: SIESTA-L@listserv.uam.es
Sent: Sunday, December 7, 2008 9:31:38 AM
Subject: Re: [SIESTA-L] ./optical e2.dat

Hi Catrina,

Once you have run input:
../input  SysLabel.EPSIMG

you need only run optical without the redirect arrow:
../optical

This will automatically read the e2.dat file and provide you with the real 
permittivity and other such things.

If you're performing a calculation on metals and you want to add the intraband 
component of the dielectric function, you can use the following to convert from 
relaxation time (in seconds ) into hartree's

H=6.626068E-34;
Elec=1.60217646E-19;
PI=3.14159265;
eV=((1/$1)*H)/(2*PI*Elec);
Har=eV/27.2113845;


Cheers,
Marty



2008/12/7 catrina desport [EMAIL PROTECTED]

To all respected siesta users,

I have compiled siesta with gfortran. After compiling optical from utility 
when I write ./optical e2.dat, I receive segmentation fault.

What's the reason for that.

Quick responce is really needed.

Regards,
Catrina


  

Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread Sushil Auluck

hi,
can you run the regular siesta (compiled with gfortran) ?
do you still get segfaults..if yes then your compilation may
not be correct.
s.auluck

--
...
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667  
Kanpur 208016 (UP)   Fax  :+91-512-6790914 
IndiaE-mail:[EMAIL PROTECTED]

FB 480 or 378   [EMAIL PROTECTED]
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
...


Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread catrina desport
Hello,

can you run the regular siesta (compiled with gfortran) ?

 yes I can. I also do not receive segfaults while I compile other .f files in 
utility, this has occured only for optical what should I change in it to get 
the run?

Regards,
Catrina





From: Sushil Auluck [EMAIL PROTECTED]
To: SIESTA-L@listserv.uam.es
Sent: Sunday, December 7, 2008 12:50:24 PM
Subject: Re: [SIESTA-L] [SUSPECTED-SPAM]  Re: [SIESTA-L] ./optical e2.dat

hi,
can you run the regular siesta (compiled with gfortran) ?
do you still get segfaults..if yes then your compilation may
not be correct.
s.auluck

-- ...
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667  Kanpur 208016 
(UP)   Fax  :+91-512-6790914 India  
  E-mail:[EMAIL PROTECTED]
FB 480 or 378  [EMAIL PROTECTED]
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html




  

Re: [SIESTA-L] [SUSPECTED-SPAM] [SIESTA-L] Question about polarization

2008-12-07 Thread Ravi Agrawal
Dr. Auluck,

Thanks a lot for your response. With this methodology, I end up getting a
value of the order of 7 C/m^2 (as opposed to reported value of 1.29 C/m^2).
So, I have been wondering about the sources of errors in my input file. A
sample is copied at the end of this mail.

I studied the affect of polarization grids and they don't seem to make much
difference. I am using a DZP basis set, with TM potentials for Zn and O
downloaded from SIESTA database (GGA/PBE).

Any other ideas on what should I be checking?

Regards,
Ravi

-
# Input file
-
# Crystal System - 6mm (Wurtzite)
# Space group - P63mc

# Systemname is a name for your conevenience
SystemName  ZnO Crystal
# SystemLabel is used to name the output files accordingly
SystemLabel zno
NumberOfAtoms   4
NumberOfSpecies 2

MeshCutoff  350 Ry

%block ChemicalSpeciesLabel
 1  30  Zn  # Species index, atomic number, species label
 2   8  O
%endblock ChemicalSpeciesLabel

AtomicCoordinatesFormat  Ang

LatticeConstant 1.00 Ang

MD.TypeofRun FC
MD.NumCGsteps 300
SolutionMethod diagon

PAO.BasisSize DZP
PAO.BasisType split #split, splitgauss, nodes, nonodes

%block PolarizationGrids
 7  3  3
 3  7  3
 3  3  7
%endblock PolarizationGrids
BornCharge True

%block k_grid_Monkhorst_Pack
 9   0   0  0.
 0   9   0  0.
 0   0   7  0
%endblock k_grid_Monkhorst_Pack

maxSCFIterations 200
xc.functional GGA
xc.authors PBE   #for GGA - PBE, revPBE, RPBE, LYP

DM.MixingWeight 0.05
DM.NumberPulay 4
DM.NumberBroyden 4

LongOutput T

%block LatticeParameters
3.28430 3.28430 5.28815 90  90  60
%endblock LatticeParameters

%block AtomicCoordinatesAndAtomicSpecies
1.64200 0.94825 2.64454 1
1.64200 0.94825 4.63445 2
0.0 0.0 0.0 1
0.0 0.0 1.99040 2
%endblock AtomicCoordinatesAndAtomicSpecies






On Fri, Dec 5, 2008 at 9:53 PM, Sushil Auluck [EMAIL PROTECTED] wrote:

 ravi,
 you are correct. make sure volume is in m^3..
 s.auluck

  Dear SIESTA users,
 
  I am trying to do the calculation of piezoelectric coefficients for bulk
  ZnO
  with a unit cell consisting of 4 atoms.
  Coefficient (d33) is calculated as the slope of polarization vs strain
  curve. Strain is dimensionless and therefore the units of d33 is same as
  that of polarization.
 
  In SIESTA output, the polarization is expressed in Debye units (1 Debye =
  3.33 X 10e-30 C-m). To convert it to C/m^2 (standard unit used for d33),
 I
  am diving by the volume of the unit cell. Is that correct or am I missing
  something?
 
  Thanks in advance.
 
  Ravi
 


 ...
 Prof. Sushil Auluck  Phone:+91-512-6797092/6148
 Department of Physics  +91-512-6798177(Home)
 Indian Institute of Technology   Cell :+91-9305548667
 Kanpur 208016 (UP)   Fax  :+91-512-6790914
 IndiaE-mail:[EMAIL PROTECTED][EMAIL 
 PROTECTED]
 ...:[EMAIL PROTECTED]
 http://www.iitk.ac.in/phy/People/phy_facvis.html
 http://www.iitk.ac.in/phy/New01/profile_SA.html
 ...
 ~



Re: [SIESTA-L] correct optical calculation

2008-12-07 Thread Marty Blaber
Hi Julie,

The scissor operator moves all the eigenvalues above the fermi energy
(chemical potential) up by the value you specify, this is to compensate for
the underestimation of the band gap. Usually you just choose it so that
you're band gap matches experiment.
The Broadening parameter specifies the size of the gaussian convolved with
the transitions, and as such also defines the number of points that appear
in the .EPSIMG file.
As a rule of thumb you should try to keep the broadening reasonably low. You
can always broaden the data further, but you can't deconvolve the gaussian
out of the data (because of the correlation between gaussian width and
number of points).
I generally use a broadening of 0.02 eV.
Don't forget that if you're dealing with metals, the plasma frequency
converges slower than the transitions, so you should use large optical mesh.
Your optical.Mesh should be the same style as you're monkhorst pack grid,
but much higher density.
To get accurate optical calculations, on gold for example, you should use a
monkhorst pack grid of about 21, but you may have to go as high as 29 if
you're unit cell is small.
%block kgrid_Monkhorst_Pack
  21   0   0   0.00
   0  21   0   0.00
   0   0  21   0.00
%endblock kgrid_Monkhorst_Pack

And then use a mesh like this:

%block Optical.Mesh
   65 65 65
%endblock Optical.Mesh

Note that you should test the convergence of these parameters. Also, the
finer that your broadening is, the more points you need in optical kspace to
get smooth data.

The real part is more difficult, if you're using metals, you will have to
guess the relaxation time. And you must check the convergence of the plasma
frequency with increasing optical mesh.

Cheers,
MArty



2008/12/7 Julie Smart [EMAIL PROTECTED]

 Hi all,

 I have read all mailing archive of Siesta and also all the tutorials and
 the power points about optical properties. Still I have problem with
 Optical.Broaden and Optical.Scissor, seems that I have no good idea what
 they do although forexample I know what gaussian broadening is. To cut it
 short, I want to know usually what ranges of these two parameters ore
 suitable for bulk, 1D and 2D structures. Also, when I can get the best shape
 of imaginary and real part of dielectric function.

 It would be an honor to receive your advice.
 Best wishes
 Julie Smart

 Caltech University
 www.*caltech*.edu






Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread Marty Blaber
Hi Catrina,
 Do you have any strange numbers in e2.dat are there any NaN's or anything?
These should give you an error, but may cause seg fault.
Worst case scenario, could you post the e2.dat here.

Cheers,
Marty


2008/12/7 catrina desport [EMAIL PROTECTED]

 Hello,

 can you run the regular siesta (compiled with gfortran) ?

  yes I can. I also do not receive segfaults while I compile other .f files
 in utility, this has occured only for optical what should I change in it
 to get the run?

 Regards,
 Catrina

 --
 *From:* Sushil Auluck [EMAIL PROTECTED]
 *To:* SIESTA-L@listserv.uam.es
 *Sent:* Sunday, December 7, 2008 12:50:24 PM
 *Subject:* Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical
 e2.dat

 hi,
 can you run the regular siesta (compiled with gfortran) ?
 do you still get segfaults..if yes then your compilation may
 not be correct.
 s.auluck

 -- ...
 Prof. Sushil Auluck  Phone:+91-512-6797092/6148
 Department of Physics  +91-512-6798177(Home)

 Indian Institute of Technology  Cell :+91-9305548667  Kanpur 208016
 (UP)  Fax  :+91-512-6790914India
 E-mail:[EMAIL PROTECTED]
 FB 480 or 378  [EMAIL PROTECTED]
 http://www.iitk.ac.in/phy/People/phy_facvis.html
 http://www.iitk.ac.in/phy/New01/profile_SA.html
 ...




Re: [SIESTA-L] correct optical calculation

2008-12-07 Thread Julie Smart
Dear Marty,

Happy to receive your guide. I have put broadening of 0.2 eV, since when I 
consider smaller amounts, the imaginary part of dielectric function goes to 
have alot of ups and downs which changes the results I expect. Should I again 
try to cgange it to smaller amounts?

Also, for 2D structure I have:

%block kgrid_Monkhorst_Pack
 8   0   0   0.00
  0  8   0   0.00
  0   0  1   0.00
%endblock kgrid_Monkhorst_Pack

So, I have chosen the mesh as:

%block Optical.Mesh
   40 40 1
%endblock Optical.Mesh

should I still change 1 to higher amounts?

Also, for the Scissor, as far as I got you we will have optical scissor = 
experimental bandgap - calculated bandgap ?

Wait for your kind advice.

Best wishes
Julie Smart

Caltech University
www.caltech.edu









From: Marty Blaber [EMAIL PROTECTED]
To: SIESTA-L@listserv.uam.es
Sent: Monday, December 8, 2008 4:07:18 AM
Subject: Re: [SIESTA-L] correct optical calculation

Hi Julie,

The scissor operator moves all the eigenvalues above the fermi energy (chemical 
potential) up by the value you specify, this is to compensate for the 
underestimation of the band gap. Usually you just choose it so that you're band 
gap matches experiment. 
The Broadening parameter specifies the size of the gaussian convolved with the 
transitions, and as such also defines the number of points that appear in the 
.EPSIMG file.
As a rule of thumb you should try to keep the broadening reasonably low. You 
can always broaden the data further, but you can't deconvolve the gaussian out 
of the data (because of the correlation between gaussian width and number of 
points). 
I generally use a broadening of 0.02 eV.
Don't forget that if you're dealing with metals, the plasma frequency converges 
slower than the transitions, so you should use large optical mesh.
Your optical.Mesh should be the same style as you're monkhorst pack grid, but 
much higher density.
To get accurate optical calculations, on gold for example, you should use a 
monkhorst pack grid of about 21, but you may have to go as high as 29 if you're 
unit cell is small.
%block kgrid_Monkhorst_Pack
  21   0   0   0.00
   0  21   0   0.00
   0   0  21   0.00
%endblock kgrid_Monkhorst_Pack

And then use a mesh like this:

%block Optical.Mesh
   65 65 65
%endblock Optical.Mesh

Note that you should test the convergence of these parameters. Also, the finer 
that your broadening is, the more points you need in optical kspace to get 
smooth data.

The real part is more difficult, if you're using metals, you will have to guess 
the relaxation time. And you must check the convergence of the plasma frequency 
with increasing optical mesh. 

Cheers,
MArty




2008/12/7 Julie Smart [EMAIL PROTECTED]

Hi all,

I have read all mailing archive of Siesta and also all the tutorials and the 
power points about optical properties. Still I have problem with 
Optical.Broaden and Optical.Scissor, seems that I have no good idea what they 
do although forexample I know what gaussian broadening is. To cut it short, I 
want to know usually what ranges of these two parameters ore suitable for bulk, 
1D and 2D structures. Also, when I can get the best shape of imaginary and real 
part of dielectric function.

It would be an honor to receive your advice.
Best wishes
Julie Smart

Caltech University
www.caltech.edu


  

Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread Marty Blaber
Hi Catrina,

The problem with your data file is that it has too many points. (The default
limit is 10 000 points)

I've edited the optical.f file to allow for 25000 points.
you can compile it using
gfortran -O4 optical.f -o optical
the O4 makes the calculation much faster.

The program should have stopped with an error saying Too many points but
this doesn't always work

I'll email the result to you personally because I don't think the list
accepts attachments that are very big.

Cheers,
Marty


2008/12/8 catrina desport [EMAIL PROTECTED]

 Hello Marty,

 Thank you for helping me.

 I didn't find Nan's in e2.file, you can see it in the enclosed. I would be
 thankful to see what is going wrong.

 Regards,
 Catrina

 --
 **




optical.tar.gz
Description: GNU Zip compressed data


Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat

2008-12-07 Thread Sushil Auluck

hi,
normally energy eigenvalues ( from linear methods) are supposed to be 
reliable

to within 1 Ry of the fermi energy. so you would expect that e2 to be ok for
up to 1 Ry. suppose you have 1000 energy eigenvalues in this range, then the
spacing (dE) is about 2/1000 = 0.002 Ry. Broadening could be 0.004 or even
larger. experiments normally have an accuracy of about 0.05 eV which is
0.004 Ry...these are rough estimates.
s.auluck

--
...
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667  
Kanpur 208016 (UP)   Fax  :+91-512-6790914 
IndiaE-mail:[EMAIL PROTECTED]

FB 480 or 378   [EMAIL PROTECTED]
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
...