[gpaw-users] kpoints error
Ali Malik
malik at mm.tu-darmstadt.de
Fri Jun 19 16:23:10 CEST 2020
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/
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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