[gpaw-users] Eigen wave-function

[Jun Yan]

Hi,

   I ran with your CO.py and CO.wave.py script, but didnt get any error
message. Maybe your problem is related to the version of gpaw or how it
is built? but I am sorry I can't help you at this level.

> 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
>
> **** CO.py (generate CO.gpw)
> ##!/usr/bin/env python
> from ase import *
> from ase.lattice.surface import *
> from ase.constraints import *
> from gpaw import *
> from gpaw.utilities.tools import cutoff2gridspacing, gridspacing2cutoff
> d = 1.1   # bondlength of hydrogen molecule
> a = 5.0   # sidelength of unit cell
> c = a / 2
> atoms = Atoms([Atom('C', [c - d / 2, c, c]),
>                      Atom('O', [c + d / 2, c, c])],
>                     cell=(a, a, a), pbc=True)
> calc = GPAW(nbands=5, h=0.2, txt=None)
> atoms.set_calculator(calc)
> # Start a calculation:
> energy = atoms.get_potential_energy()
> # Save wave functions:
> calc.write('CO.gpw', 'all')
>
>
> *** CO.wave.py (to generate a charge cube file and wave function for k=0
> band=1)
> ##!/usr/bin/env python
> from ase import *
> from ase.lattice.surface import *
> from ase.constraints import *
> from gpaw import *
> from gpaw.utilities.tools import cutoff2gridspacing, gridspacing2cutoff
> basename = 'CO'
> # load nc binary file and get calculator
> atoms, calc = restart(basename + '.gpw')
> n = calc.get_all_electron_density(gridrefinement=2)
>
> chg=basename+'.chg.cube'
> write(chg,atoms , data=n)
>
> k=0
> band=1
> wf1=calc.wfs.kpt_u[k].psit_nG[band],
> fname1=basename+'.1.'+str(k)+'.'+str(band)+'.cube'
> write(fname1, atoms, data=wf1)
>
> wf2 = calc.get_pseudo_wave_function(band=band,kpt=k)
> fname1=basename+'.2.'+str(k)+'.'+str(band)+'.cube'
> write(fname2, atoms, data=wf2)
>
> Note: I have never successfully get the 2nd wave function wf2.
> --------------------------------------------------
> 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
>>
>>
>>
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>>
>>
>