[gpaw-users] [ase-users] Any calculator add-ons?
Jess Wellendorff Pedersen
jesswe at fysik.dtu.dk
Thu Apr 7 12:38:39 CEST 2011
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
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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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