[gpaw-users] The ELF function

[Kacprzak, Katarzyna]

Hi,

So here what I get when I try to use each command:

>> calc = GPAW('Na.gpw')
>> atom = calc.get_atoms()

 >>>from gpaw.elf import *
 >>> elf = ELF(calc)
 >>> print elf
<gpaw.elf.ELF instance at 0x2c90ae9248>

 >>> elf.initialize(calc)
 >>> print elf.initialize(calc)
None

 >>> elf.update(calc.wfs)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/v/linux26_x86_64/appl/nano/gpaw/svn//lib/python/gpaw/elf.py",  
line 103, in update
    wfs.add_to_kinetic_density_from_k_point(self.taut_sG[0], kpt)
  File "/v/linux26_x86_64/appl/nano/gpaw/svn//lib/python/gpaw/ 
wavefunctions.py", line 1084, in add_to_kinetic_density_from_k_point
    raise RuntimeError('Wavefunctions have not been initialized.')
RuntimeError: Wavefunctions have not been initialized.


It also doesn't change the fact that in the first script I get wrong  
values (not from 0 to 1, but from 0 to 0.465)

Best regards,


On Mar 12, 2010, at 11:09 AM, Jens Jørgen Mortensen wrote:

> On Thu, 2010-03-11 at 18:24 +0200, Kacprzak, Katarzyna wrote:
>> Hi,
>>
>> I have been trying to analyze some of my results with electron
>> localization function. Since the analysis gave strange results, I  
>> have
>> tried to run this analysis for Na atom. I attached figures with two
>> different results for Na.
>>
>> Thus, one result obtain using this part of code:
>>
>> ------------------------------------------------------------------------------
>> name = 'Na'
>> atom = Atoms (read (name +".xyz"))
>>
>> atom.set_cell([7.92, 7.92, 7.92])
>> calc = GPAW(h=0.18, nbands=-10, xc='PBE', txt=name+'.out')
>> atom.set_calculator(calc)
>> atom.get_potential_energy()
>>
>> from gpaw.elf import *
>> elf = ELF(calc)
>>
>> elf.initialize(calc)
>> elf.update(calc.wfs)
>>
>> elf_out = elf.get_electronic_localization_function(gridrefinement=2)
>> write ('Na.plt', molecule, data=elf_out)
>>
>> ------------------------------------------------------------------------------
>>
>> and another was obtain, just by restarting gpw file. Thus, with this
>> code:
>>
>> ------------------------------------------------------------------------------
>> from ase import *
>> from gpaw import *
>>
>>
>> calc = GPAW('Na.gpw')
>> atom = calc.get_atoms()
>>
>> from gpaw.elf import *
>> elf = ELF(calc)
>>
>> elf_out = elf.get_electronic_localization_function(gridrefinement=2)
>> write ('Na_2.plt', atom, data=elf_out)
>
> In your second script, you left out the two lines:
>
> elf.initialize(calc)
> elf.update(calc.wfs)
>
> Are they not needed when you restart from a file?
>
> JJ
>
>>
>> ------------------------------------------------------------------------------
>> Each of these scripts gave two different results. First one, gave
>> values from 0 to 0.456, and the second, gave values from 0 to 1. Even
>> though the second gave correct values, plotting them I obtain
>> localization far away from the atom... I attached the figure to this
>> email. The "A" figure is related to the first case, the "B"- is
>> related to the second case. Both of the figures are plotted for
>> maximal values (A for 0.456, and B for 1)
>>
>> I will be grateful for any suggestions how to fix this problem and  
>> get
>> correct analysis from GPAW.
>>
>> I have also compared the elf for another system using Octopus, and
>> GPAW. And again I obtain two different results (from Octopus results
>> are correct).
>>
>> Best regard,
>>
>> Katarzyna Kacprzak
>>
>> katarzyna.a.kacprzak at jyu.fi
>>
>> PhD student
>> Nanoscience Center
>> Univeristy of Jyvaskyla
>>
>>
>>
>> _______________________________________________
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>