[ase-users] Any calculator add-ons?
Augustus Low
mrspiko at gmail.com
Thu Apr 7 11:41:33 CEST 2011
Hi Jess,
Thanks for the great tip! =) But now after doing what you do, I don't have
that error anymore. However this was returned:
File "<stdin>", line 1, in <module>
File "/home/lowt0008/ase/ase/atoms.py", line 494, in get_potential_energy
return self.calc.get_potential_energy(self)
File
"/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/aseinterface.py",
line 32, in get_potential_energy
self.calculate(atoms, converge=True)
File "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py",
line 226, in calculate
self.set_positions(atoms)
File "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py",
line 301, in set_positions
spos_ac = self.initialize_positions(atoms)
File "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py",
line 293, in initialize_positions
self.wfs.set_positions(spos_ac)
File
"/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/fd.py",
line 45, in set_positions
FDPWWaveFunctions.set_positions(self, spos_ac)
File
"/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py",
line 41, in set_positions
WaveFunctions.set_positions(self, spos_ac)
File
"/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/base.py",
line 226, in set_positions
rank_a = self.gd.get_ranks_from_positions(spos_ac)
File
"/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/domain.py", line
102, in get_ranks_from_positions
assert (rnk_ac >= 0).all() and (rnk_ac < self.parsize_c).all()
AssertionError
On Thu, Apr 7, 2011 at 5:32 PM, Jess Wellendorff Pedersen <
jesswe at fysik.dtu.dk> wrote:
> slight correction: nbands of course concerns only the valence electrons,
> i.e. those not included in the GPAW setups...
>
> /Jess
>
> Augustus Low wrote:
>
>> Hi ZhenHua,
>>
>> When I ran GPAW and tried to calculate the potential energy, giving it
>> nbands = 10, the computer returned this.
>>
>> File "<stdin>", line 1, in <module>
>> File "/home/lowt0008/ase/ase/atoms.py", line 494, in get_potential_energy
>> return self.calc.get_potential_energy(self)
>> File
>> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/aseinterface.py",
>> line 32, in get_potential_energy
>> self.calculate(atoms, converge=True)
>> File "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py",
>> line 225, in calculate
>> self.initialize(atoms)
>> File "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py",
>> line 441, in initialize
>> % (nvalence, nbands))
>> ValueError: Too few bands! Electrons: 99, bands: 10
>>
>> Any idea what this means? Also, what does the nbands in the GPAW mean?
>> I just want to thank you in advance.
>>
>> Regards,
>> Augustus
>>
>>
>> Sorry to trouble you again.
>> On Mon, Apr 4, 2011 at 12:23 AM, ZhenHua Zeng <zhenhua.zeng at fysik.dtu.dk<mailto:
>> zhenhua.zeng at fysik.dtu.dk>> wrote:
>>
>> Hi Augustus,
>>
>> Yes. You need to install the calculators in ASE before using
>> except EMT, which is like a toy included in the ASE package.
>>
>> Dacapo (Jacapo in ase3) is a total energy program based on
>> density functional theory.
>> It uses a plane wave basis for the valence electronic states and
>> describes the core-electron interactions with
>> Vanderbilt ultrasoft pseudo-potentials (USPP). Dacapo has been
>> implemented widely in the studies of surface
>> physics/chemistry, condensed physics, catalysis etc. It have been
>> proved to be a reliable code to describe
>> the properties in these relevant field.
>>
>> Besides, GPAW, another DFT code, is a more promising code In ASE
>> interface.
>> It is based on the projector-augmented wave (PAW), which is more
>> sophisticated than USPP method used in Dacapo.
>>
>> So for Dacapo and GPAW, we would like to recommend the latter
>> for your study.
>> For more detail, please refer the link below.
>>
>> https://wiki.fysik.dtu.dk/ase/ase/calculators/calculators.html#module-calculators
>>
>> Best wishes!
>> ZhenHua
>> On 2011/4/2 4:12, Augustus Low wrote:
>>
>>> Hi Zhenhua,
>>>
>>> Meaning with whatever calculators I need, I need to install them?
>>> Besides EMT, are there any other calculators that are included in
>>> the python ase package?
>>>
>>> Regards,
>>> Augustus
>>>
>>> On Fri, Apr 1, 2011 at 4:43 AM, ZhenHua Zeng
>>> <zhenhua.zeng at fysik.dtu.dk <mailto:zhenhua.zeng at fysik.dtu.dk>> wrote:
>>>
>>> Hi Augustus,
>>>
>>> You need to install them before importing and using them.
>>> You can find the introduction of installment in the website
>>> of codes,
>>> which are also linked from front page of ase
>>> https://wiki.fysik.dtu.dk/ase/.
>>>
>>> Best wishes!
>>> ZhenHua
>>>
>>>
>>> On 2011/3/31 17:18, Augustus Low wrote:
>>>
>>>> Hi ZhengHua,
>>>>
>>>> Thank you for your help. Any idea how I can import these
>>>> calculators and use them? Meaning like the command codes?
>>>>
>>>> Grateful,
>>>> Augustus
>>>>
>>>> On Thu, Mar 31, 2011 at 4:06 PM, ZhenHua Zeng
>>>> <zhenhua.zeng at fysik.dtu.dk
>>>> <mailto:zhenhua.zeng at fysik.dtu.dk>> wrote:
>>>>
>>>> Hi Augustus,
>>>>
>>>> As much as i know, there are few empirical potential
>>>> codes working on ionic crystal.
>>>> DFT codes are supposed to work well on ionic crystal.
>>>> And there is so much variety, such as GPAW or Dacapo etc
>>>> in ASE.
>>>>
>>>> Best wishes!
>>>> ZhenHua
>>>>
>>>> On 2011/3/31 4:23, Augustus Low wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I'm trying to simulate the potential energies for both
>>>>> hydroxyapatite and fluorapatite. However I'm unable to
>>>>> calculate their potential energies because the EMT
>>>>> calculator does not support the calculations of the P,
>>>>> F and Ca elements. Any idea if other calculators can
>>>>> help solve this problem?
>>>>>
>>>>> Regards,
>>>>> Augustus
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ase-users mailing list
>>>>> ase-users at listserv.fysik.dtu.dk <mailto:
>>>>> ase-users at listserv.fysik.dtu.dk>
>>>>>
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>>>
>>>>
>>>>
>>>> -- ZhenHua Zeng
>>>> Technical University of Denmark
>>>> Department of Physics
>>>> Building 307, Room 242
>>>> DK-2800 Kongens Lyngby
>>>> Denmark
>>>> Mob.: (+45) 5278 0888 <tel:%28%2B45%29%205278%200888>
>>>> Tel.: (+45) 4525 3234 <tel:%28%2B45%29%204525%203234>
>>>> Fax.: (+45) 4593 2399 <tel:%28%2B45%29%204593%202399>
>>>> Email: Zhenhua.Zeng at fysik.dtu.dk <mailto:
>>>> Zhenhua.Zeng at fysik.dtu.dk>
>>>>
>>>> ---------------------------------
>>>>
>>>>
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>>>
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>>
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>
> --
> Jess Wellendorff Pedersen
>
> ph.d student
> Center for Atomic-scale Materials Design (CAMD)
> Department of Physics
> Technical University of Denmark (DTU)
>
>
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