[gpaw-users] kpoints error

[Ask Hjorth Larsen]

Am Fr., 19. Juni 2020 um 16:24 Uhr schrieb Ali Malik via gpaw-users
<gpaw-users at listserv.fysik.dtu.dk>:
>
> Dear all,
>
> I am trying to do ionic relaxation on VF3 compound.  But I keep getting an error in kpoints (probably) during setting up of the k-mesh. I am not sure if this is related to ase or gpaw.
>
> Here is the output.
>
> File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/bin/gpaw", line 11, in <module>
>     load_entry_point('gpaw==20.1.0', 'console_scripts', 'gpaw')()
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/cli/main.py", line 80, in main
>     ase_main('gpaw', 'GPAW command-line tool', __version__, commands, hook)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/cli/main.py", line 99, in main
>     f(args)
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/cli/python.py", line 34, in run
>     runpy.run_path(args.arguments[0], run_name='__main__')
>   File "/shared/apps/.intel/2018/python/3.7.2/lib/python3.7/runpy.py", line 263, in run_path
>     pkg_name=pkg_name, script_name=fname)
>   File "/shared/apps/.intel/2018/python/3.7.2/lib/python3.7/runpy.py", line 96, in _run_module_code
>     mod_name, mod_spec, pkg_name, script_name)
>   File "/shared/apps/.intel/2018/python/3.7.2/lib/python3.7/runpy.py", line 85, in _run_code
>     exec(code, run_globals)
>   File "optimizeall.py", line 44, in <module>
>     rel_ions.run(fmax=fmax)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/optimize/optimize.py", line 272, in run
>     return Dynamics.run(self)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/optimize/optimize.py", line 162, in run
>     for converged in Dynamics.irun(self):
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/optimize/optimize.py", line 128, in irun
>     self.atoms.get_forces()
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/atoms.py", line 754, in get_forces
>     forces = self._calc.get_forces(self)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/calculators/calculator.py", line 659, in get_forces
>     return self.get_property('forces', atoms)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/calculators/calculator.py", line 695, in get_property
>     self.calculate(atoms, [name], system_changes)
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/calculator.py", line 288, in calculate
>     self.initialize(atoms)
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/calculator.py", line 682, in initialize
>     cell_cv, pbc_c, N_c)
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/calculator.py", line 1027, in create_wave_functions
>     kd = self.create_kpoint_descriptor(nspins)
>   File "/home/groups/da_mm/codes/gpaw/gpaw-20.1.0/lib/python3.7/site-packages/gpaw-20.1.0-py3.7-linux-x86_64.egg/gpaw/calculator.py", line 995, in create_kpoint_descriptor
>     bzkpts_kc = kpts2ndarray(par.kpts, atoms)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/calculators/calculator.py", line 339, in kpts2ndarray
>     return kpts2kpts(kpts, atoms=atoms).kpts
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/calculators/calculator.py", line 329, in kpts2kpts
>     return KPoints(monkhorst_pack(size) + offsets)
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/ase/dft/kpoints.py", line 17, in monkhorst_pack
>     kpts = np.indices(size).transpose((1, 2, 3, 0)).reshape((-1, 3))
>   File "/shared/apps/.intel/2019/python/3.7.2/lib/python3.7/site-packages/numpy/core/numeric.py", line 1703, in indices
>     dimensions = tuple(dimensions)
> TypeError: 'int' object is not iterable

kpoints needs to be three numbers or a dictionary.

Best regards
Ask

>
>
> And here is the calculation script.
>
>
> from ase.io import read, write
> from gpaw import GPAW, PW
> #import gpaw_functions_dev as gf
> from ase.parallel import parprint
> from ase.optimize.bfgs import BFGS
> import numpy as np
>
> # ionic, cell, full relaxation, iterative relaxation
>
>
>
> # script related
> verbose = True
>
> # GPAW parameters
> filename = "BPOSCAR"
> kden = 5
> kpden = {"size": kden}
> encut = 500
> eigensolver = "rmm-diis"
> relal = "BFGS"
> swidth = 0.04
> xc = "PBE"
> fmax = 0.01
>
> # output
> fout = "relaxed_atoms"
>
> # Read structure
> atoms = read(filename, format="vasp")
>
> # calculator
> calc = GPAW(mode=PW(ecut=encut),
>         xc=xc,
>         kpts=kpden,
>         eigensolver=eigensolver,
>         occupations={"name": "fermi-dirac", "width": swidth},
>         txt="rel-ions.txt")
>
> atoms.set_calculator(calc)
> # first_ionic
> #gf.optimize(atoms, reltype="ions",  relaxalgorithm=relal,  fmax=fmax)
> rel_ions = BFGS(atoms, logfile="rel-ionic.log")
> rel_ions.run(fmax=fmax)
>
> Also, the structure file is attached. I have no idea about the cause of this error.
>
>
> Best Regards,
> Ali
>
>
>
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