date:20160216

Re: [Wien] basic-question-about-PORT-mini

2016-02-16 Thread Fecher, Gerhard

The series of subroutines is easy,
The main program is obviously mini
this calls haupt


How much do you know about Fortran ?

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: wien-boun...@zeus.theochem.tuwien.ac.at 
[wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von ‪Amir lot‬ ‪‬ 
[lot.a...@yahoo.com]
Gesendet: Mittwoch, 17. Februar 2016 04:36
An: wien@zeus.theochem.tuwien.ac.at
Betreff: Re: [Wien] basic-question-about-PORT-mini

Dear Prof. Blaha and and Prof. Marks,
Thanks for your reply.
But i think the main step of min_lapw program is "SRC_mini".
I have checked it ( SRC_mini) for several times but i could not understand it
because the job of subroutines are not clear.
For example, which program reads or makes struct file or which one checks 
symmetry for generates equivalent positions and ...

With best,
Amir
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Re: [Wien] basic-question-about-PORT-mini

2016-02-16 Thread ‪Amir lot‬ ‪

Dear Prof. Blaha and and Prof. Marks,Thanks for your reply.But i think the main 
step of min_lapw program is "SRC_mini".I have checked it ( SRC_mini) for 
several times but i could not understand it because the job of subroutines are 
not clear.For example, which program reads or makes struct file or which one 
checks symmetry for generates equivalent positions and ...
With best,Amir    ___
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Re: [Wien] basic-question-about-PORT-mini

2016-02-16 Thread Peter Blaha


The whole procedure is managed by the script min_lapw.

It starts an scf cycle (run_lapw ...)
then it calls   the  program mini  (x mini)
and this program reads the struct file and forces (also of previous 
steps) and eventually uses the PORT method to calculate the new atomic 
positions (including the proper symmetry) and writes a new case.struct file.
min_lapw then initiatess another scf cycle and this goes on untile 
forces are small.


Am 16.02.2016 um 18:49 schrieb ‪Amir lot‬ ‪:

Dear Prof. L. Marks,
Thanks for your reply.
Can I know the steps of your PORT-program step by step along with the
job that step/program does?
If it is possible please as:
For example : XXX program reads struct file and 
YYY program gets Energy and 
ZZZ program checks symmetry ..

With best,
Amir


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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] basic-question-about-PORT-mini

2016-02-16 Thread Laurence Marks

Sorry, but this is asking a bit too much. You should read the code.


---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A

On Tue, Feb 16, 2016 at 11:49 AM, ‪Amir lot‬ ‪‬  wrote:

> Dear Prof. L. Marks,
> Thanks for your reply.
> Can I know the steps of your PORT-program step by step along with the job
> that step/program does?
> If it is possible please as:
> For example : XXX program reads struct file and 
> YYY program gets Energy and 
> ZZZ program checks symmetry ..
>
> With best,
> Amir
>
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Re: [Wien] basic-question-about-PORT-mini

2016-02-16 Thread ‪Amir lot‬ ‪

Dear Prof. L. Marks,Thanks for your reply.Can I know the steps of your 
PORT-program step by step along with the job that step/program does?If it is 
possible please as:For example : XXX program reads struct file and YYY 
program gets Energy and ZZZ program checks symmetry ..
With best,Amir
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Re: [Wien] Weird wannier functions coming out from wien2wannier

2016-02-16 Thread Elias Assmann

Pablo,

On 02/15/2016 05:17 PM, Pablo Villar Arribi wrote:
> Any ideas on why this different behaviour between Wien2k and Quantum
> Espresso? Could it be due to the intrinsic diferences between an
> all-electron code and a pseudopotential code in terms of their Bloch
> states, which are used as a starting point for Wannier90?

I think it is much more likely to be a problem in wplot [unfortunately
for me :-)]. In particular, it sounds like you have a good projections,
but something is going wrong in the plotting itself.

Here are some suggestions:

1. By way of general advice, I suggest to start with a coarse r-mesh
(e.g. 10×10×10 points) and a larger plot region than you think you need,
to figure out the correct plotting window. You said you checked this,
but it can really be tricky, what with different settings both in
Wannier90 (translate_home_cell) and wplot2xsf (-noshift). Once you have
that, you can scale up the precision.

2. All parts of the calculation (mainly, case.chk and case.vector) have
to match. If, for some reason, you ran another lapw1 after wannier90,
wplot will not work. Therefore, it sometimes helps simply to repeat the
whole procedure (lapw1 && w2w && wannier90 && wplot), just to be sure
that there is no inconsistency.

3. Did you check if the real-space representation of the WF is real
(i.e., case.psink should be 0 or ±π up to numerical precision)? Because
the xsf format does not accomodate complex numbers, wplot2xsf by default
writes |w(r)|² sgn Re w(r). This could lead to “strange” isosurfaces if
there is a phase.

4. If the above does not help and you just want your plots, it could be
an option to simply use the ones from Quantum Espresso. In my view,
real-space WFs are a qualitative rather than a quantitative tool (unless
you are very careful …), therefore it could be okay to use the QE
real-space WFs as a visualization for your Wien2k WFs, as long as H(R)
and the band structure are “the same”. Obviously, this depends on what
you want to do with them.

5. On the other hand, if you want to get it right with Wien2k (and
possibly help me find a bug), the next thing I would try is a different
version of wplot (I am assuming that you tried the one included in
Wien2k 14.2). This is one part of the package that I changed quite a
lot recently and invariably, bugs creep in. You could either try the
newest version from GitHub (caveat: the format of case.inwplot changed)
where some of those bugs are fixed; or the “old” one (0.97, available
at
http://www.ifp.tuwien.ac.at/forschung/arbeitsgruppen/cms/software-download/wien2wannier/),
which has a different set of bugs.

6. Relatedly, what crystal structure do you have? Wien2Wannier has had
some problems with more “difficult” lattice types in the past.

Good luck,

Elias

--
Elias Assmann

Wien2Wannier: maximally localized Wannier functions
from linearized augmented plane waves

http://wien2wannier.github.io/
https://github.com/wien2wannier/wien2wannier/

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Re: [Wien] basic-question-about-mini-PORT

2016-02-16 Thread Laurence Marks

Inlined


---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A

On Mon, Feb 15, 2016 at 11:08 PM, ‪Amir lot‬ ‪‬  wrote:

> Dear WIEN2k users,
> As I can guess mini or PORT program works as:
> The program gets Energy ( and forces) of compound and positions of atoms
> which have forces.
> PORT program using these data provides next new positions related to atoms
> which have forces.
> using new generated struct file with new positions, the PORT program does
> a scf.
> Now, The program gets new energy of compound with new positions of atoms
> which have forces and produces next new positions.
> The PORT repeats the above steps till forces drops  below for example 1 .
>
>
> First question
> Are the above steps correct?
>

Yes

>
> second question
> How does PORT produces equivalent positions related to new positions When
> the program want to generate the new struct file with new positions?
>

It uses the symmetry relations between the positions which are at the end
of case.struct

>
> Third question
> When the positions of atom are as X=Y=Z, Does PORT program get only energy
> and for example X position or energy and (X,Y,Z) positions as input data?
> Because when (X=Y=Z) and PORT program get (X,Y,Z) as a input data may
> produces new positions as (Xn#Yn#Zn) which make error because (X=Y=Z).
>

Port obeys the symmetry relationships. If due to these X=Y=Z the atomic
positions always obey this constraint. If no symmetry forces this the
positions may change so this is no longer an equality. Symmetry rules.

N.B., MSR1a is similar, but does not use the forces in the same way and
ignores the energy.

>
>
> With best,
> Amir
>
>
>
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Re: [Wien] scf2forces

2016-02-16 Thread Michael Sluydts

At risk of stating the obvious: the fact that the folder is called win2k 
and not wien2k also seems mildly suspicious.


On 2/16/2016 2:28 PM, Gavin Abo wrote:
If you do "ls 
~/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python", does 
it show files like api_gruneisen.py?


If the files like that are in the python folder in the lib64 
directory, then your .bashrc looks fine.  On my system, they are under 
lib instead of lib64:


username@computername:~$ ls ~/phonopy-1.10.0/lib/python/phonopy
api_gruneisen.py   api_qha.pyc  harmonic  _phonopy.so units.pyc
api_gruneisen.pyc  cui  __init__.py   qha version.py
api_phonopy.py file_IO.py   __init__.pyc  _spglib.so version.pyc
api_phonopy.pycfile_IO.pyc  interface structure
api_qha.py gruneisenphononunits.py

In the error message, it looks like it is pointing to the wrong 
location (/home/IITJHOME/ambeshst/win2k13mpi/phonopy), when it should 
be pointing to 
"/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python".


Do "echo $PYTHONPATH", is it pointing to the right location?

On my system, it is pointing to 
"/home/username/phonopy-1.10.0/lib/python":


username@computername:~$ echo $PYTHONPATH
:/home/username/phonopy-1.10.0/lib/python

After adding export lines to .bashrc and saving the changes, did you 
reload the .bashrc (using "source ~/.bashrc" or open and use a new 
terminal)?


On 2/16/2016 2:49 AM, Rajneesh Chaurasiya wrote:
I have modified the file according to your suggestion but still there 
is same error...


Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
from phonopy import *
ImportError: No module named phonopy


I am attaching the .bashrc file so please check whether this is 
correct or not..

please suggest your suggestion..


On Sat, Feb 13, 2016 at 12:38 PM, Rajneesh Chaurasiya 
 wrote:




Dear Gavin,

I have installed newer version of phonopy package

https://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz/download
and it required the scf2forces which i get from
http://www.wien2k.at/reg_user/unsupported/ but it showing the
error, which i have seen in the previous message. but as per your
suggestion if i use he experimental support option in Phonopy
1.10.0 [
http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]:
means phonopy --wien2k -f case-001.scf case-002.scf then it
showing error some error.


Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
from phonopy import *
ImportError: No module named phonopy


 so i dont know that the installed phonopy is compatible with the
wien2k or not.

please give me your ideas why this is happening.




--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
ABV-IIITM, Gwalior, India
Mob. No. +91-9584499697
  +91-8435727031



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ir. Michael Sluydts
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Technologiepark 903
9052 Zwijnaarde, Belgium
tel. +32 (0)9 264 66 19
https://molmod.ugent.be

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Re: [Wien] scf2forces

2016-02-16 Thread Gavin Abo

If you do "ls 
~/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python", does 
it show files like api_gruneisen.py?


If the files like that are in the python folder in the lib64 directory, 
then your .bashrc looks fine.  On my system, they are under lib instead 
of lib64:


username@computername:~$ ls ~/phonopy-1.10.0/lib/python/phonopy
api_gruneisen.py   api_qha.pyc  harmonic  _phonopy.so units.pyc
api_gruneisen.pyc  cui  __init__.py   qha version.py
api_phonopy.py file_IO.py   __init__.pyc  _spglib.so version.pyc
api_phonopy.pycfile_IO.pyc  interface structure
api_qha.py gruneisenphononunits.py

In the error message, it looks like it is pointing to the wrong location 
(/home/IITJHOME/ambeshst/win2k13mpi/phonopy), when it should be pointing 
to "/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python".


Do "echo $PYTHONPATH", is it pointing to the right location?

On my system, it is pointing to "/home/username/phonopy-1.10.0/lib/python":

username@computername:~$ echo $PYTHONPATH
:/home/username/phonopy-1.10.0/lib/python

After adding export lines to .bashrc and saving the changes, did you 
reload the .bashrc (using "source ~/.bashrc" or open and use a new 
terminal)?


On 2/16/2016 2:49 AM, Rajneesh Chaurasiya wrote:
I have modified the file according to your suggestion but still there 
is same error...


Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
from phonopy import *
ImportError: No module named phonopy


I am attaching the .bashrc file so please check whether this is 
correct or not..

please suggest your suggestion..


On Sat, Feb 13, 2016 at 12:38 PM, Rajneesh Chaurasiya 
> wrote:




Dear Gavin,

I have installed newer version of phonopy package

https://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz/download
and it required the scf2forces which i get from
http://www.wien2k.at/reg_user/unsupported/ but it showing the
error, which i have seen in the previous message. but as per your
suggestion if i use he experimental support option in Phonopy
1.10.0 [
http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]:
means phonopy --wien2k -f case-001.scf case-002.scf then it
showing error some error.


Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
from phonopy import *
ImportError: No module named phonopy


 so i dont know that the installed phonopy is compatible with the
wien2k or not.

please give me your ideas why this is happening.




--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
ABV-IIITM, Gwalior, India
Mob. No. +91-9584499697
  +91-8435727031
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Re: [Wien] scf2forces

2016-02-16 Thread Rajneesh Chaurasiya

I have modified the file according to your suggestion but still there is
same error...

Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
from phonopy import *
ImportError: No module named phonopy


I am attaching the .bashrc file so please check whether this is correct or
not..
please suggest your suggestion..


On Sat, Feb 13, 2016 at 12:38 PM, Rajneesh Chaurasiya  wrote:

>
>
> Dear Gavin,
>
> I have installed newer version of phonopy package
> https://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz/download
> and it required the scf2forces which i get from
> http://www.wien2k.at/reg_user/unsupported/ but it showing the error,
> which i have seen in the previous message. but as per your suggestion if i
> use he experimental support option in Phonopy 1.10.0 [
> http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]: means
> phonopy --wien2k -f case-001.scf case-002.scf then it showing error some
> error.
>
>
> Traceback (most recent call last):
>   File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
> from phonopy import *
> ImportError: No module named phonopy
>
>
>  so i dont know that the installed phonopy is compatible with the wien2k
> or not.
>
> please give me your ideas why this is happening.
>



-- 
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
ABV-IIITM, Gwalior, India
Mob. No. +91-9584499697
  +91-8435727031


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Re: [Wien] basic-question-about-PORT-mini

Re: [Wien] basic-question-about-PORT-mini

Re: [Wien] basic-question-about-PORT-mini

Re: [Wien] basic-question-about-PORT-mini

Re: [Wien] basic-question-about-PORT-mini

Re: [Wien] Weird wannier functions coming out from wien2wannier

Re: [Wien] basic-question-about-mini-PORT

Re: [Wien] scf2forces

Re: [Wien] scf2forces

Re: [Wien] scf2forces

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