[gpaw-users] [ase-users] Any calculator add-ons?
Jess Wellendorff
jesswellendorff at gmail.com
Sat Apr 9 11:48:42 CEST 2011
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 <mailto: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>
> <mailto: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>>
> <mailto: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>>>
> <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
> <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>>>
> <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
> <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>>>
> <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
> <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
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> Denmark
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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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