[gpaw-users] Eigen wave-function

[Duy Le]

Thank you all.
The extra ',' was fixed and it produced correct wave grid now.
However, the wf2 could not be written out although I have changed
fname2(actually, when I combined 2 .py file together, I did not modify
it correctly). Anyway, as I can get the wavefunction by using
calc.wfs.kpt_u[k].psit_nG[band], I can ignore this error for now.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, Apr 22, 2010 at 3:36 AM, Jussi Enkovaara <jussi.enkovaara at csc.fi> wrote:
> Duy Le wrote:
>>
>> Thank you. It produced with calc.wfs.kpt_u[ikpt].psit_nG[iband],
>> However, there seems to be a problem. The header of cube file is
>> different from that of charge cube file. I beleive that they must be
>> identical. Could you please explain to me what is written in wave
>> function cube file?
>
>> ******Charge cube file's header:
>> cube file from ase
>> OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
>>    2    0.000000    0.000000    0.000000
>>   48    0.196846    0.000000    0.000000
>>   48    0.000000    0.196846    0.000000
>>   48    0.000000    0.000000    0.196846
>>    6    0.000000    3.684966    4.724315    4.724315
>>    8    0.000000    5.763664    4.724315    4.724315
>> ***wave function cube file's header:
>> cube file from ase
>> OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
>>    2    4.724315    0.000000    0.000000
>>    1    4.724315    0.000000    0.000000
>>   24    0.000000    0.393693    0.000000
>>   24    0.000000    0.000000    0.393693
>>    6    0.000000    3.684966    4.724315    4.724315
>>    8    0.000000    5.763664    4.724315    4.724315
>
> The headers (48 vs. 24) are different as for the charge density you use
> twice as dense grid as for the
> wave functions (gridrefinement=2) in your script. Furthermore, your script
> contains small bug (see below)
> which explains the dimension 1 in the second line of the wave function cube
> file.
>
>> wf1=calc.wfs.kpt_u[k].psit_nG[band],
>
> You have an extra ',' in the end of line, and as result you do not obtain
> the correct 3D wave function
> data.
>
>> wf2 = calc.get_pseudo_wave_function(band=band,kpt=k)
>> fname1=basename+'.2.'+str(k)+'.'+str(band)+'.cube'
>> write(fname2, atoms, data=wf2)
>
> Here, "fname2" is not defined and the script exits with an error.
>
> After the above corrections I was able to run your scripts and obtain
> reasonable looking plots.
> Also other bands than the second (notice that indexing starts from 0, thus
> band=1 gives the second
> band) seemed to work. I used relatively recent GPAW version 0.7.6336M.
>
> Best regards,
> Jussi
>
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Wed, Apr 21, 2010 at 1:58 PM, Jun Yan <juya at fysik.dtu.dk> wrote:
>>>
>>> Hi,
>>>
>>>   Did you use calc.write('filename.gpw'.'all') command to write down the
>>> wavefunctions ?
>>>   If you did and still have problems,  can you attach your python file
>>> that
>>> used to generate this error ?
>>>
>>>   A direct way to get the wavefunction is
>>> calc.wfs.kpt_u[ikpt].psit_nG[iband],
>>>   while ikpt and iband are the number of kpoints and bands for the
>>> wavefunctions you want to get.
>>>   Hope this helps.
>>>
>>> All the best,
>>> Jun Yan
>>>
>>> Duy Le wrote:
>>>
>>> Thanks. I have looked at that tutorial. I have never successfully
>>> obtained the wave function in cube format. It always ended up with the
>>> error "shape mismatch: objects cannot be broadcast to a single shape"
>>> (I asked yesterday, see in the end of this email).
>>> However, even if I successfully get cube file, I beleive that this
>>> will give Square of wavefunction. I want wavefunction only for my
>>> other analysis.
>>>
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>>  File "CO.wave.py", line 15, in ?
>>>   wf = calc.get_pseudo_wave_function(band=band)
>>>  File "/home/duyle/usr/lib64/python/gpaw/aseinterface.py", line 348, in
>>> get_pse
>>> udo_wave_function
>>>   pad=False)
>>>  File "/home/duyle/usr/lib64/python/gpaw/aseinterface.py", line 353, in
>>> get_pse
>>> udo_wave_function
>>>   psit_G = self.wfs.get_wave_function_array(band, kpt, spin)
>>>  File "/home/duyle/usr/lib64/python/gpaw/wavefunctions.py", line 405, in
>>> get_wa
>>> ve_function_array
>>>   psit_G = self.gd.collect(psit1_G)
>>>  File "/home/duyle/usr/lib64/python/gpaw/grid_descriptor.py", line 373,
>>> in
>>> coll
>>> ect
>>>   A_xg[..., b0:e0, b1:e1, b2:e2] = a_xg
>>> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>>> ----------------------------------------------------------------------
>>> --------------------------------------------------
>>> Duy Le
>>> PhD Student
>>> Department of Physics
>>> University of Central Florida.
>>>
>>> "Men don't need hand to do things"
>>>
>>>
>>>
>>> On Wed, Apr 21, 2010 at 12:19 PM, Ask Hjorth Larsen <askhl at fysik.dtu.dk>
>>> wrote:
>>>
>>>
>>> Dear Duy Le
>>>
>>>
>>>
>>> Dear all,
>>> I wonder if it is possible to get KS wave functions with gpaw? I want
>>> KS wave function to perform post processing.
>>>
>>>
>>> You can find an example in the wave function plotting tutorial:
>>>
>>>
>>> https://wiki.fysik.dtu.dk/gpaw/tutorials/plotting/plot_wave_functions.html
>>>
>>> This will get the pseudo wave functions, not the all-electron ones.  The
>>> all-electron ones are normally too nasty.
>>>
>>> Regards
>>> Ask
>>>
>>>
>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>>
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