[gpaw-users] [ase-users] Any calculator add-ons?
Augustus Low
mrspiko at gmail.com
Fri Apr 8 17:53:35 CEST 2011
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
>> <mailto:Zhenhua.Zeng at fysik.dtu.dk>
>> <mailto:Zhenhua.Zeng at fysik.dtu.dk
>> <mailto: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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>>
>> ---------------------------------
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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)
>>
>>
>>
>>
>>
>>
>> -- 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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