[gpaw-users] GLLBSC using PW mode
Jens Jørgen Mortensen
jjmo at dtu.dk
Fri Aug 9 08:07:20 CEST 2019
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>> 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>> 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>
>> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>> >
>>
>
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