[gpaw-users] LCAO mode + Ni basis + large system error
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Tue Nov 19 15:14:32 CET 2013
Hi,
please see
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2013-June/002126.html
and a longer explanation why basis sets distributed with 0.9 version of
setups are incorrect:
http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2013-May/002084.html
If you use any of the elements mentioned under "Modified setups" at
https://wiki.fysik.dtu.dk/gpaw/devel/releasenotes.html#development-version-in-trunk
which have f-polarization function in the basis, please generate the
basis set as described here:
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2012-April/001394.html
Best regards,
Marcin
On 11/19/2013 12:40 PM, Chengjun Jin wrote:
> Hi again,
>
> I just notice that with the new SETUP 0.9 for Ni, semi-core 3p are put
> into valence. Therefore, we get f-function included in DZP basis.
>
> Still good to know what's happening with the f-function in this case?
>
>
>
> PBE Basis functions for Ni
> ==========================
>
> Basis functions for l=0, n=4
> ----------------------------
>
> Zeta 1: softly confined pseudo wave, fixed energy shift
> DE=0.011 eV :: rc=10.89 Bohr
> Potential amp=12.00 :: ri/rc=0.60
> Norm=1.029
>
> Zeta 2: split-valence wave, fixed tail norm
> Tail norm 0.162 :: rsplit=5.38 Bohr
>
> Basis functions for l=1, n=3
> ----------------------------
>
> Zeta 1: softly confined pseudo wave, fixed energy shift
> DE=0.011 eV :: rc=3.56 Bohr
> Potential amp=12.00 :: ri/rc=0.60
> Norm=0.226
>
> Zeta 2: split-valence wave, fixed tail norm
> Tail norm 0.161 :: rsplit=2.19 Bohr
>
> Basis functions for l=2, n=3
> ----------------------------
>
> Zeta 1: softly confined pseudo wave, fixed energy shift
> DE=0.011 eV :: rc=6.35 Bohr
> Potential amp=12.00 :: ri/rc=0.60
> Norm=0.468
>
> Zeta 2: split-valence wave, fixed tail norm
> Tail norm 0.161 :: rsplit=3.31 Bohr
>
> Polarization function: l=3, rc=6.35
> -----------------------------------
> ------------------------------------------------------------------------
> *From:* gpaw-users-bounces at listserv.fysik.dtu.dk
> [gpaw-users-bounces at listserv.fysik.dtu.dk] on behalf of Chengjun Jin
> [chej at fysik.dtu.dk]
> *Sent:* Tuesday, November 19, 2013 11:16 AM
> *To:* gpaw-users at listserv.fysik.dtu.dk
> *Subject:* [gpaw-users] LCAO mode + Ni basis + large system error
>
> Dear All,
>
> I got errors when I did a standard DFT on a large system with DZP
> basis (see the error and inputs below, the structure is attached).
>
> Some facts:
> *The error occurs only in LCAO mode, not FD mode.
> *If I reduce the basis set from 'dzp' to 'sz', it works well.
> *With 'dzp' basis, If I replace Ni by Au, it also works.
>
> I guess it may relate to the Ni basis set. Any idea to fix it?
>
> Regards,
> Chengjun
>
> ##################### inputs
> 7 from ase.io import read, write
> 8 from ase.visualize import view
> 9
> 10 from gpaw import GPAW, Mixer, FermiDirac
> 11 from gpaw.lcao.tools import dump_hamiltonian_parallel as dhp
> 12
> 13
> 14 scat= read('scat.traj')
> 15
> 16 scat.set_initial_magnetic_moments([0,]*len(scat))
> 17 #view(scat)
> 18
> 19 #setup the basis
> 20 #inter = range(67, 89) #XXX The internal region
> 21 #mol = range(68, 88) #XXX Molecule region
> 22 basis = {None: 'dzp'}
> 23 #for a in inter:
> 24 # basis[a] = 'szp'
> 25 #for a in mol:
> 26 # basis[a] = 'dz'
> 27 #
> 28 #setup the calc
> 29 calc = GPAW(mode='lcao',
> 30 h=0.2,
> 31 xc='PBE',
> 32 txt='scat.txt',
> 33 occupations=FermiDirac(0.1),
> 34 basis=basis,
> 35 usesymm=False, # number of kpt
> 36 kpts=(4, 4, 1), #careful about direction.
> 37 mixer=Mixer(0.05, 5, 100.0)
> 38 )
> 39
> 40 scat.set_calculator(calc)
> 41 scat.get_potential_energy()
> 42 fermi = calc.get_fermi_level()
> 43 print >> open('scat_fermi.txt', 'w'), repr(fermi)
> 44 calc.write('scat.gpw')
>
>
>
>
> ################################errors
> errors from --dry-run:
> ################################
>
> Traceback (most recent call last):
> File "scat.py", line 41, in <module>
> scat.get_potential_energy()
> File "/home/camp/chej/bin/ase.3066/ase/atoms.py", line 627, in
> get_potential_energy
> return self._calc.get_potential_energy(self)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/aseinterface.py", line
> 38, in get_potential_energy
> self.calculate(atoms, converge=True)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/paw.py", line 229, in
> calculate
> self.initialize(atoms)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/paw.py", line 562, in
> initialize
> self.wfs = LCAOWaveFunctions(lcaoksl, *args)
> File
> "/home/niflheim/chej/bin/gpaw.10126/gpaw/wavefunctions/lcao.py", line
> 59, in __init__
> self.tci = NewTCI(gd.cell_cv, gd.pbc_c, setups, kd.ibzk_qc, kd.gamma)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 721, in __init__
> self.calculate_expansions()
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 749, in calculate_expansions
> l_Ij, phit_Ijq)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 525, in calculate_expansions
> tsoe = calc.calculate_expansions(l1_j, f1_jq, l2_j, f2_jq)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 488, in calculate_expansions
> oe = self.transformer.calculate_overlap_expansion(a_q, la, lb)
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 456, in calculate_overlap_expansion
> a_g = (8 * fbt(l, a_q * k1**(-2 - lmax - l), self.k_q, R) /
> File "/home/niflheim/chej/bin/gpaw.10126/gpaw/lcao/overlap.py", line
> 99, in fbt
> ifft(C[l][n] * f * r**(1 + l - n), 2 * m)[:m].real)
> IndexError: list index out of range
> GPAW CLEANUP for serial binary: <type 'exceptions.IndexError'>
> occured. Calling sys.exit()
>
>
>
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