[gpaw-users] GLLBSC using PW mode
Jens Jørgen Mortensen
jjmo at dtu.dk
Tue Aug 13 10:30:17 CEST 2019
On 8/9/19 2:27 PM, Jingjing SHAO wrote:
> I am running it on 96 cores. Is that a issue? For some cases, it works
> but for some it does not. So I do not really get the reason.
> In attachment you will find two txt file, One works for the delta xc,
> one does not. Hope it could help to find the issue.
It seems that this bug has been fixed in the latest version of GPAW.
Try updating to version 19.8.1 and let us know if there are any problems
still.
Jens Jørgen
>
> Thank you very much for taking the time!
>
> Jingjing
>
> On Fri, 9 Aug 2019 at 08:06, Jens Jørgen Mortensen <jjmo at dtu.dk
> <mailto:jjmo at dtu.dk>> wrote:
>
> On 8/8/19 10:49 AM, Jingjing SHAO via gpaw-users wrote:
> > Dear Jens,
> >
> > i have a following question about GLLBSC in PW mode.
> > When I want to get the delta xc after the ground state
> calculation is
> > finished. It gives following error:
>
> Can you attach the text output from your calculation (GLLBSC.txt)? On
> how many cores did you run this? (it works OK on 4 cores with latest
> version of GPAW).
>
> Jens Jørgen
>
> > ------
> > rank=68 L00: Traceback (most recent call last):
> > rank=68 L01: File
> >
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/__init__.py",
>
> > line 200, in main
> > rank=68 L02: runpy.run_path(gpaw_args.script,
> run_name='__main__')
> > rank=68 L03: File
> > "/sw/tools/python/2.7.13.scal./mpp1/lib/python2.7/runpy.py", line
> 252,
> > in run_path
> > rank=68 L04: return _run_module_code(code, init_globals,
> run_name,
> > path_name)
> > rank=68 L05: File
> > "/sw/tools/python/2.7.13.scal./mpp1/lib/python2.7/runpy.py", line
> 82, in
> > _run_module_code
> > rank=68 L06: mod_name, mod_fname, mod_loader, pkg_name)
> > rank=68 L07: File
> > "/sw/tools/python/2.7.13.scal./mpp1/lib/python2.7/runpy.py", line
> 72, in
> > _run_code
> > rank=68 L08: exec code in run_globals
> > rank=68 L09: File "gs.py", line 36, in <module>
> > rank=68 L10: EKs, Dxc =
> response.calculate_delta_xc_perturbation()
> > rank=68 L11: File
> >
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/c_response.py",
>
> > line 364, in calculate_delta_xc_perturbation
> > rank=68 L12:
> gaps.append(self.calculate_delta_xc_perturbation_spin(s))
> > rank=68 L13: File
> >
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/c_response.py",
>
> > line 324, in calculate_delta_xc_perturbation_spin
> > rank=68 L14: self.wfs.add_orbital_density(nt_G, kpt, lumo_n)
> > rank=68 L15: File
> >
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/wavefunctions/pw.py",
>
> > line 618, in add_orbital_density
> > rank=68 L16: axpy(1.0, abs(self.pd.ifft(kpt.psit_nG[n],
> kpt.q))**2,
> > nt_G)
> > rank=68 L17: IndexError: index 39 is out of bounds for axis 0
> with size 2
> > GPAW CLEANUP (node 68): <type 'exceptions.IndexError'> occurred.
> > Calling MPI_Abort!
> > ----
> >
> > It says something about spin, seems. But in my script, I have
> > atoms.set_initial_magnetic_moments(np.zeros(len(atoms)) and
> spinpol =
> > False, so i have not considered the spin cases.
> > There is anything I could do in order to get the calculation running?
> >
> >
> > Thanks a lot and I appreciate your patience and time.
> >
> > Best regards,
> > Jingjing
> >
> >
> > On Wed, 7 Aug 2019 at 07:40, Jens Jørgen Mortensen <jjmo at dtu.dk
> <mailto:jjmo at dtu.dk>
> > <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>>> wrote:
> >
> > On 8/6/19 3:42 PM, Jingjing SHAO wrote:
> >> It is gpaw-1.4.0.
> >> Without the line, it works now. Thank you very much!
> >
> >
> > Great!
> >
> >
> >>
> >> Jingjing
> >>
> >> On Mon, 5 Aug 2019 at 12:57, Jens Jørgen Mortensen
> <jjmo at dtu.dk <mailto:jjmo at dtu.dk>
> >> <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>>> wrote:
> >>
> >> On 7/29/19 4:51 PM, Jingjing SHAO via gpaw-users wrote:
> >> > Dear GPAW-USERS,
> >> >
> >> > i got an Value Error that I could not understand by using
> >> GLLBSC in PW
> >> > mode.
> >> > """"
> >> > rank=61 L10: atoms.get_potential_energy()
> >> > rank=56 L28: self.calculate_impl(gd, n_sg, v_sg, e_g)
> >> > rank=64 L25: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/wavefunctions/pw.py",
> >>
> >> > line 1598, in update_pseudo_potential
> >> > rank=56 L29: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/nonlocalfunctional.py",
> >>
> >> > line 58, in calculate_impl
> >> > rank=61 L11: File
> >> >
> >>
> "/sw/chem/ase/3.16.0/mpp1/lib/python2.7/site-packages/ase-3.16.0-py2.7.egg/ase/atoms.py",
> >>
> >> > line 685, in get_potential_energy
> >> > rank=64 L26: nt_dist_xg, vxct_dist_xg)
> >> > rank=56 L30: self.calculate_spinpaired(e_g, n_sg[0],
> >> v_sg[0])
> >> > rank=61 L12: energy =
> self._calc.get_potential_energy(self)
> >> > rank=64 L27: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/functional.py",
> >>
> >> > line 52, in calculate
> >> > rank=56 L31: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/nonlocalfunctional.py",
> >>
> >> > line 72, in calculate_spinpaired
> >> > rank=61 L13: File
> >> >
> >>
> "/sw/chem/ase/3.16.0/mpp1/lib/python2.7/site-packages/ase-3.16.0-py2.7.egg/ase/calculators/calculator.py",
> >>
> >> > line 448, in get_potential_energy
> >> > rank=64 L28: self.calculate_impl(gd, n_sg, v_sg, e_g)
> >> > rank=56 L32:
> contribution.calculate_spinpaired(e_g, n_g,
> >> v_g)
> >> > rank=61 L14: energy = self.get_property('energy',
> atoms)
> >> > rank=56 L33: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/c_gllbscr.py",
> >>
> >> > line 156, in calculate_spinpaired
> >> > rank=64 L29: File
> >> >
> >>
> "/sw/chem/gpaw/1.4.0/mpp1/lib/python2.7/site-packages/gpaw/xc/gllb/nonlocalfunctional.py",
> >>
> >> > line 58, in calculate_impl
> >> > rank=61 L15: File
> >> >
> >>
> "/sw/chem/ase/3.16.0/mpp1/lib/python2.7/site-packages/ase-3.16.0-py2.7.egg/ase/calculators/calculator.py",
> >>
> >> > line 493, in get_property
> >> > rank=56 L34: self.e_g[:] = np.where(n_g<self.damp, 0,
> >> self.e_g)
> >> > rank=64 L30: self.calculate_spinpaired(e_g, n_sg[0],
> >> v_sg[0])
> >> > rank=61 L16: self.calculate(atoms, [name],
> system_changes)
> >> > rank=56 L35: ValueError: operands could not be broadcast
> >> together with
> >> > shapes (18,24,18) () (72,96,112)
> >> > """"
> >> > The used script and the calculated structure are
> attached.
> >> Could you
> >> > mind to help me to point out the exact problem?
> >>
> >> What version of GPAW is this?
> >>
> >> Maybe {'augment_grids': True} does not work with GLLBSC.
> Could
> >> you try
> >> to comment out that line?
> >>
> >> Jens Jørgen
> >>
> >> >
> >> > Thank you very much.
> >> >
> >> > Best regards,
> >> > Jingjing Shao
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > gpaw-users mailing list
> >> > gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>
> >> <mailto:gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> >> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
> >> >
> >>
> >
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