[gpaw-users] [ase-users] Any calculator add-ons?
Augustus Low
mrspiko at gmail.com
Sun Apr 10 11:06:04 CEST 2011
Hi Jess,
Thank you for your help. I think I kinda get what you mean. However does
this mean that calculating the bulk potential energy of a Hydroxyapatite
structure would not impossible?
Regards,
Augustus
On Sat, Apr 9, 2011 at 5:48 PM, Jess Wellendorff
<jesswellendorff at gmail.com>wrote:
> Yes, by instructing GPAW to let the electronic structure in the unit cell
> be that of an infinitely periodic system in all directions, you actually
> model the full bcc lattice by using only a single unit cell decorated with
> the correct basis of atoms, i.e. for a qubic bcc cell this is two atoms.
> That is the correct way of doing electronic structure calculations for a
> perfect lattice (no defects etc.).
>
> However, for these calculations to accurately model a full lattice, i.e. to
> accurately represent the periodicity, you need the calculations to sample
> k-space as well as the usual real-space. As seen on the GPAW wiki-pages,
> this is done by "kpts=(x,x,x)" where x are integers greater than zero. If
> you calculate some quantity, e.g. the cohesive energy, of your bcc lattice
> for increasing number of k-points you will most often find that the computed
> quantity converges to some stationary value as you increase the number of
> points you sample in k-space. This tells you the minimum number of k-points
> to use in order to accurately model the bcc lattice.
>
> /Jess
>
> Den 08-04-2011 17:53, Augustus Low skrev:
>
> Hi Jess,
>
> Thanks for the advice. I just want to clarify certain points.
> By using pbc=(1,1,1), i'll actually have the full bcc structure?
>
> Regards,
> Augustus
>
> On Thu, Apr 7, 2011 at 6:38 PM, Jess Wellendorff Pedersen <
> jesswe at fysik.dtu.dk> wrote:
>
>> Hi augustus,
>>
>> I'm not really certain what you are aiming at with this script, but there
>> are at least a few issues with it:
>>
>> Augustus Low wrote:
>>
>>> Hi Jess,
>>>
>>> This is my script:
>>>
>>> from ase import Atoms
>>> from ase.visualize import view
>>> from ase.calculators.emt import EMT
>>> from ase.constraints import FixAtoms
>>> from ase.optimize import QuasiNewton
>>> from ase.lattice.cubic import BodyCenteredCubic
>>>
>>> a = 3.61
>>> bcc = BodyCenteredCubic(size=(1,1,1), symbol='Cu', pbc=(1,1,0),
>>> latticeconstant=3.61)
>>>
>> this creates a bcc unit cell for you with two atoms in it and periodic
>> boundary conditions in the x and y directions but not in the z direction.
>> Doesn't really apply for an infinitely extended solid, for which pbc should
>> be (1,1,1). pbc = (1,1,0) is mostly applicable to surface slab models and
>> the likes.
>>
>>
>>> bcc.append(29)
>>> bcc.positions[2]=(a,a,a)
>>> bcc.append(29)
>>> bcc.positions[3]=(a,0,0)
>>> bcc.append(29)
>>> bcc.positions[4]=(0,0,a)
>>> bcc.append(29)
>>> bcc.positions[5]=(a,0,a)
>>> bcc.append(29)
>>> bcc.positions[6]=(0,a,0)
>>> bcc.append(29)
>>> bcc.positions[7]=(0,a,a)
>>> bcc.append(29)
>>> bcc.positions[8]=(a,a,0)
>>>
>> this is where it gets really problematic. All the above appends are bad,
>> because the periodic boundary conditions "translate" the unit cell for you
>> in the pbc=1 directions. Therefore, with a manual translation in say the x
>> direction, you now put two atoms exactly on top of each other in the
>> pbc=True directions.
>>
>>
>>> constraint = FixAtoms(mask=[a.symbol !='Cu' for a in bcc])
>>> bcc.set_constraint(constraint)
>>>
>>> view(bcc)
>>>
>>> bcc.set_calculator(EMT())
>>> dyn = QuasiNewton(bcc)
>>> dyn.run(fmax=0.05)
>>>
>>> print bcc.get_potential_energy()
>>>
>>> from gpaw import GPAW
>>> calc = GPAW(nbands= -10)
>>> bcc.set_calculator(calc)
>>> bcc.get_potential_energy()
>>>
>> I hope you realize that this would be an extremely crude DFT calculation,
>> with default real-space density grid spacing, LDA exchange-correlation, and
>> only a single k-point (the gamma point) in reciprocal space, meaning that
>> even though you a using periodic boundary conditions such as to model an
>> extended lattice you are not taking this periodicity into account in the
>> electronic structure calculation.
>>
>> /Jess
>>
>>>
>>> On Thu, Apr 7, 2011 at 5:47 PM, Jess Wellendorff Pedersen <
>>> jesswe at fysik.dtu.dk <mailto:jesswe at fysik.dtu.dk>> wrote:
>>>
>>> could you send me the script you try to run?
>>>
>>> /Jess
>>>
>>>
>>> Jess Wellendorff Pedersen wrote:
>>>
>>> did you run the GPAW test suite ?
>>>
>>> Augustus Low wrote:
>>>
>>> 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 <mailto:jesswe at fysik.dtu.dk>
>>> <mailto:jesswe at fysik.dtu.dk <mailto: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>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>
>>> <mailto: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>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>
>>> <mailto: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>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>>
>>> <mailto:zhenhua.zeng at fysik.dtu.dk
>>> <mailto:zhenhua.zeng at fysik.dtu.dk>
>>> <mailto: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
>>>
>>>
>>>
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>>>
>>>
>>>
>>> -- 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:%28%2B45%29%205278%200888>
>>> <tel:%28%2B45%29%205278%200888>
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>>> Email: Zhenhua.Zeng at fysik.dtu.dk
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>>> <mailto:Zhenhua.Zeng at fysik.dtu.dk
>>> <mailto:Zhenhua.Zeng at fysik.dtu.dk>>
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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)
>>>
>>>
>>>
>>>
>>>
>>>
>>> -- Jess Wellendorff Pedersen
>>>
>>> ph.d student
>>> Center for Atomic-scale Materials Design (CAMD)
>>> Department of Physics
>>> Technical University of Denmark (DTU)
>>>
>>>
>>>
>> --
>> 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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