[gpaw-users] kpoints error

[Ali Malik]

Thanks for pointing out the mistake. It should have been 'density' 
instead of 'size'.

Best Regards,
Ali

On 19/06/2020 20:19, Ask Hjorth Larsen wrote:
> 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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