[gpaw-users] Error in band-parallelization
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Mon Dec 3 14:29:30 CET 2012
Hi,
On 12/03/12 13:53, mohnish pandey wrote:
> Dear GPAW users,
>
> I am trying to calculate the energy of some reference system like P84,
> S32, Se64 etc. Number of k-points in the cell is less so I have to
> parallelize over bands. But I am getting the following error for the
> same. I get the similar error for other large systems when using
> band-parallelization. Thanks a lot in advance for help :)
>
> *Error:*
>
> Traceback (most recent call last):
> File "Se64.py", line 52, in ?
> en = Se64.get_potential_energy()
> File "/home/camp/mohpa/ase/ase/atoms.py", line 608, in
> get_potential_energy
> return self._calc.get_potential_energy(self)
> File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py",
> line 38, in get_potential_energy
> self.calculate(atoms, converge=True)
> File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 267, in calculate
> self.occupations):
> File "/home/niflheim/mohpa/gpaw/gpaw/scf.py", line 46, in run
> wfs.eigensolver.iterate(hamiltonian, wfs)
> File "/home/niflheim/mohpa/gpaw/gpaw/eigensolvers/eigensolver.py",
> line 60, in iterate
> e, psit_nG = self.iterate_one_k_point(hamiltonian, wfs, kpt)
> File "/home/niflheim/mohpa/gpaw/gpaw/eigensolvers/cg.py", line 51,
> in iterate_one_k_point
> R_nG = reshape(self.Htpsit_nG, psit_nG.shape)
> File "/home/niflheim/mohpa/gpaw/gpaw/hs_operators.py", line 13, in
> reshape
> return a_x.ravel()[:np.prod(shape)].reshape(shape)
> AttributeError: 'NoneType' object has no attribute 'ravel'
>
cg does not work with band parallelization - in PW mode the only
possibility is to use rmm-diis.
Best regards,
Marcin
>
> *The input file is:*
>
> Se64= read('/home/camp/mohpa/ref_ener/cif-files-nsp/Se.cif', index=-1,
> format='cif')
>
> length_a = (np.dot(Se64.get_cell()[0],Se64.get_cell()[0]))**0.5
> length_b = (np.dot(Se64.get_cell()[1],Se64.get_cell()[1]))**0.5
> length_c = (np.dot(Se64.get_cell()[2],Se64.get_cell()[2]))**0.5
>
> kx = int(33.0/length_a+0.5)
> ky = int(33.0/length_b+0.5)
> kz = int(33.0/length_c+0.5)
>
> calc = GPAW(mode=PW(600),
> xc = 'PBE',
> kpts=(kx,ky,kz),
> usesymm=True,
> parallel={'domain':None},
> # parallel={'band':1},
> maxiter=600,
> eigensolver='cg',
> txt = 'Se64_opt_bulk_PBE.out',
> occupations=FermiDirac(width=0.05))
>
> Se64.set_calculator(calc)
> en = Se64.get_potential_energy()
> calc.write('Se64'+'_PBE.gpw')
> p = paropen('tot_en.txt','a')
> p.write('Se64'+' '+str(en)+'\n')
>
> *The .cif file:*
>
> #\#CIF1.1
> ##########################################################################
> # Crystallographic Information Format file
> # Produced by PyCifRW module
> #
> # This is a CIF file. CIF has been adopted by the International
> # Union of Crystallography as the standard for data archiving and
> # transmission.
> #
> # For information on this file format, follow the CIF links at
> # http://www.iucr.org
> ##########################################################################
>
> data_Se
> _symmetry_space_group_name_H-M 'P 1'
> _cell_length_a 10.1538633861
> _cell_length_b 15.30902371
> _cell_length_c 15.7391813737
> _cell_angle_alpha 90.0
> _cell_angle_beta 94.042869363
> _cell_angle_gamma 90.0
> _chemical_name_systematic 'Generated by pymatgen'
> _symmetry_Int_Tables_number 1
> _chemical_formula_structural Se
> _chemical_formula_sum Se64
> _cell_volume 2440.50047819
> _cell_formula_units_Z 64
> loop_
> _symmetry_equiv_pos_site_id
> _symmetry_equiv_pos_as_xyz
> 1 'x, y, z'
>
> loop_
> _atom_site_type_symbol
> _atom_site_label
> _atom_site_symmetry_multiplicity
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_attached_hydrogens
> _atom_site_B_iso_or_equiv
> _atom_site_occupancy
> Se Se1 1 0.171579 0.824628 0.086415 0 . 1
> Se Se2 1 0.951916 0.857563 0.814616 0 . 1
> Se Se3 1 0.364628 0.236288 0.691437 0 . 1
> Se Se4 1 0.849520 0.713948 0.526390 0 . 1
> Se Se5 1 0.347639 0.990287 0.906751 0 . 1
> Se Se6 1 0.120869 0.714049 0.984712 0 . 1
> Se Se7 1 0.602871 0.354499 0.525862 0 . 1
> Se Se8 1 0.451916 0.642437 0.814616 0 . 1
> Se Se9 1 0.620869 0.785951 0.984712 0 . 1
> Se Se10 1 0.671579 0.675372 0.086415 0 . 1
> Se Se11 1 0.897129 0.854499 0.474138 0 . 1
> Se Se12 1 0.222771 0.047426 0.230452 0 . 1
> Se Se13 1 0.135372 0.736288 0.308563 0 . 1
> Se Se14 1 0.048084 0.142437 0.185384 0 . 1
> Se Se15 1 0.548084 0.357563 0.185384 0 . 1
> Se Se16 1 0.657733 0.524822 0.353788 0 . 1
> Se Se17 1 0.264540 0.593959 0.013428 0 . 1
> Se Se18 1 0.235460 0.093959 0.986572 0 . 1
> Se Se19 1 0.521092 0.690537 0.193152 0 . 1
> Se Se20 1 0.937050 0.410578 0.695855 0 . 1
> Se Se21 1 0.758361 0.453780 0.475644 0 . 1
> Se Se22 1 0.562950 0.910578 0.304145 0 . 1
> Se Se23 1 0.102871 0.145501 0.525862 0 . 1
> Se Se24 1 0.225499 0.508143 0.238152 0 . 1
> Se Se25 1 0.379131 0.214049 0.015288 0 . 1
> Se Se26 1 0.062950 0.589422 0.304145 0 . 1
> Se Se27 1 0.978908 0.190537 0.806848 0 . 1
> Se Se28 1 0.847639 0.509713 0.906751 0 . 1
> Se Se29 1 0.241639 0.546220 0.524356 0 . 1
> Se Se30 1 0.152361 0.490287 0.093249 0 . 1
> Se Se31 1 0.842267 0.024822 0.646212 0 . 1
> Se Se32 1 0.111019 0.284823 0.231350 0 . 1
> Se Se33 1 0.999752 0.685345 0.644476 0 . 1
> Se Se34 1 0.342267 0.475178 0.646212 0 . 1
> Se Se35 1 0.879131 0.285951 0.015288 0 . 1
> Se Se36 1 0.652361 0.009713 0.093249 0 . 1
> Se Se37 1 0.437050 0.089422 0.695855 0 . 1
> Se Se38 1 0.021092 0.809463 0.193152 0 . 1
> Se Se39 1 0.500248 0.185345 0.355524 0 . 1
> Se Se40 1 0.388981 0.784823 0.768650 0 . 1
> Se Se41 1 0.864628 0.263712 0.691437 0 . 1
> Se Se42 1 0.150480 0.286052 0.473610 0 . 1
> Se Se43 1 0.277229 0.547426 0.769548 0 . 1
> Se Se44 1 0.258361 0.046220 0.475644 0 . 1
> Se Se45 1 0.725499 0.991857 0.238152 0 . 1
> Se Se46 1 0.349520 0.786052 0.526390 0 . 1
> Se Se47 1 0.397129 0.645501 0.474138 0 . 1
> Se Se48 1 0.735460 0.406041 0.986572 0 . 1
> Se Se49 1 0.157733 0.975178 0.353788 0 . 1
> Se Se50 1 0.328421 0.324628 0.913585 0 . 1
> Se Se51 1 0.777229 0.952574 0.769548 0 . 1
> Se Se52 1 0.774501 0.491857 0.761848 0 . 1
> Se Se53 1 0.611019 0.215177 0.231350 0 . 1
> Se Se54 1 0.478908 0.309463 0.806848 0 . 1
> Se Se55 1 0.828421 0.175372 0.913585 0 . 1
> Se Se56 1 0.650480 0.213948 0.473610 0 . 1
> Se Se57 1 0.274501 0.008143 0.761848 0 . 1
> Se Se58 1 0.722771 0.452574 0.230452 0 . 1
> Se Se59 1 0.888981 0.715177 0.768650 0 . 1
> Se Se60 1 0.764540 0.906041 0.013428 0 . 1
> Se Se61 1 0.000248 0.314655 0.355524 0 . 1
> Se Se62 1 0.741639 0.953780 0.524356 0 . 1
> Se Se63 1 0.499752 0.814655 0.644476 0 . 1
> Se Se64 1 0.635372 0.763712 0.308563 0 . 1
>
>
> --
> Regards,
> MOHNISH,
> -----------------------------------------------------------------
> Mohnish Pandey,
> PhD Student,
> Center for Atomic Scale Materials Design,
> Department of Physics,
> Technical University of Denmark
> -----------------------------------------------------------------
>
>
>
> _______________________________________________
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> gpaw-users at listserv.fysik.dtu.dk
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--
***********************************
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
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