[gpaw-users] Hubbard U parameter
Punit Kumar
ip.punit.2016 at gmail.com
Mon Sep 30 15:24:05 CEST 2024
Hello Jens,
Thank you for your reply. The full trace back error message is mentioned
below:
rank=07 L00: Traceback (most recent call last):
rank=07 L01: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/__init__.py",
line 216, in main
rank=07 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
rank=07 L03: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 265,
in run_path
rank=07 L04: return _run_module_code(code, init_globals, run_name,
rank=07 L05: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 97,
in _run_module_code
rank=07 L06: _run_code(code, mod_globals, init_globals,
rank=07 L07: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 87,
in _run_code
rank=07 L08: exec(code, run_globals)
rank=08 L00: Traceback (most recent call last):
rank=07 L09: File "ucf.py", line 36, in <module>
rank=07 L10: opt.run(fmax=0.05)
rank=08 L01: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/__init__.py",
line 216, in main
rank=07 L11: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 275, in run
rank=08 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
rank=07 L12: return Dynamics.run(self)
rank=08 L03: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 265,
in run_path
rank=07 L13: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 162, in run
rank=08 L04: return _run_module_code(code, init_globals, run_name,
rank=07 L14: for converged in Dynamics.irun(self):
rank=08 L05: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 97,
in _run_module_code
rank=07 L15: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 128, in irun
rank=07 L16: self.atoms.get_forces()
rank=07 L17: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/atoms.py",
line 791, in get_forces
rank=08 L06: _run_code(code, mod_globals, init_globals,
rank=07 L18: forces = self._calc.get_forces(self)
rank=06 L00: Traceback (most recent call last):
rank=08 L07: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 87,
in _run_code
rank=07 L19: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/abc.py",
line 23, in get_forces
rank=06 L01: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/__init__.py",
line 216, in main
rank=08 L08: exec(code, run_globals)
rank=07 L20: return self.get_property('forces', atoms)
rank=06 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
rank=08 L09: File "ucf.py", line 36, in <module>
rank=07 L21: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/calculator.py",
line 736, in get_property
rank=06 L03: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 265,
in run_path
rank=08 L10: opt.run(fmax=0.05)
rank=07 L22: self.calculate(atoms, [name], system_changes)
rank=06 L04: return _run_module_code(code, init_globals, run_name,
rank=08 L11: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 275, in run
rank=07 L23: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 322, in calculate
rank=06 L05: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 97,
in _run_module_code
rank=08 L12: return Dynamics.run(self)
rank=06 L06: _run_code(code, mod_globals, init_globals,
rank=07 L24: for _ in self.icalculate(atoms, properties,
system_changes):
rank=08 L13: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 162, in run
rank=06 L07: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 87,
in _run_code
rank=07 L25: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 345, in icalculate
rank=08 L14: for converged in Dynamics.irun(self):
rank=06 L08: exec(code, run_globals)
rank=07 L26: self.set_positions(atoms)
rank=08 L15: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 128, in irun
rank=06 L09: File "ucf.py", line 36, in <module>
rank=07 L27: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 545, in set_positions
rank=08 L16: self.atoms.get_forces()
rank=06 L10: opt.run(fmax=0.05)
rank=07 L28: nlcao, nrand = self.wfs.initialize(self.density,
self.hamiltonian,
rank=08 L17: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/atoms.py",
line 791, in get_forces
rank=06 L11: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 275, in run
rank=07 L29: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/wavefunctions/fdpw.py",
line 307, in initialize
rank=08 L18: forces = self._calc.get_forces(self)
rank=06 L12: return Dynamics.run(self)
rank=07 L30: hamiltonian.update(density)
rank=08 L19: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/abc.py",
line 23, in get_forces
rank=06 L13: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 162, in run
rank=07 L31: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 232, in update
rank=08 L20: return self.get_property('forces', atoms)
rank=06 L14: for converged in Dynamics.irun(self):
rank=07 L32: atomic_energies = self.update_corrections(density, W_aL)
rank=08 L21: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/calculator.py",
line 736, in get_property
rank=06 L15: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 128, in irun
rank=07 L33: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 290, in update_corrections
rank=08 L22: self.calculate(atoms, [name], system_changes)
rank=06 L16: self.atoms.get_forces()
rank=07 L34: eU, dHU_sp = hubbard(setup, D_sp)
rank=08 L23: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 322, in calculate
rank=06 L17: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/atoms.py",
line 791, in get_forces
rank=07 L35: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hubbard.py",
line 13, in hubbard
rank=08 L24: for _ in self.icalculate(atoms, properties,
system_changes):
rank=06 L18: forces = self._calc.get_forces(self)
rank=07 L36: nn = (2 * np.array(l_j) + 1)[0:nl[0]].sum()
rank=08 L25: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 345, in icalculate
rank=07 L37: IndexError: index 0 is out of bounds for axis 0 with size 0
rank=06 L19: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/abc.py",
line 23, in get_forces
rank=08 L26: self.set_positions(atoms)
rank=06 L20: return self.get_property('forces', atoms)
rank=08 L27: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 545, in set_positions
rank=06 L21: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/calculator.py",
line 736, in get_property
rank=08 L28: nlcao, nrand = self.wfs.initialize(self.density,
self.hamiltonian,
rank=06 L22: self.calculate(atoms, [name], system_changes)
rank=08 L29: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/wavefunctions/fdpw.py",
line 307, in initialize
rank=06 L23: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 322, in calculate
rank=08 L30: hamiltonian.update(density)
rank=06 L24: for _ in self.icalculate(atoms, properties,
system_changes):
rank=08 L31: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 232, in update
rank=06 L25: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 345, in icalculate
rank=08 L32: atomic_energies = self.update_corrections(density, W_aL)
rank=06 L26: self.set_positions(atoms)
GPAW CLEANUP (node 7): <class 'IndexError'> occurred. Calling MPI_Abort!
rank=08 L33: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 290, in update_corrections
rank=06 L27: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 545, in set_positions
rank=08 L34: eU, dHU_sp = hubbard(setup, D_sp)
rank=06 L28: nlcao, nrand = self.wfs.initialize(self.density,
self.hamiltonian,
rank=08 L35: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hubbard.py",
line 13, in hubbard
rank=06 L29: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/wavefunctions/fdpw.py",
line 307, in initialize
rank=08 L36: nn = (2 * np.array(l_j) + 1)[0:nl[0]].sum()
rank=06 L30: hamiltonian.update(density)
rank=08 L37: IndexError: index 0 is out of bounds for axis 0 with size 0
rank=06 L31: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 232, in update
rank=06 L32: atomic_energies = self.update_corrections(density, W_aL)
rank=06 L33: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 290, in update_corrections
rank=06 L34: eU, dHU_sp = hubbard(setup, D_sp)
rank=06 L35: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hubbard.py",
line 13, in hubbard
rank=06 L36: nn = (2 * np.array(l_j) + 1)[0:nl[0]].sum()
rank=06 L37: IndexError: index 0 is out of bounds for axis 0 with size 0
GPAW CLEANUP (node 8): <class 'IndexError'> occurred. Calling MPI_Abort!
GPAW CLEANUP (node 6): <class 'IndexError'> occurred. Calling MPI_Abort!
rank=09 L00: Traceback (most recent call last):
rank=09 L01: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/__init__.py",
line 216, in main
rank=09 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
rank=09 L03: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 265,
in run_path
rank=09 L04: return _run_module_code(code, init_globals, run_name,
rank=09 L05: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 97,
in _run_module_code
rank=09 L06: _run_code(code, mod_globals, init_globals,
rank=09 L07: File "/opt/python/3.8.5.0/lib/python3.8/runpy.py", line 87,
in _run_code
rank=09 L08: exec(code, run_globals)
rank=09 L09: File "ucf.py", line 36, in <module>
rank=09 L10: opt.run(fmax=0.05)
rank=09 L11: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 275, in run
rank=09 L12: return Dynamics.run(self)
rank=09 L13: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 162, in run
rank=09 L14: for converged in Dynamics.irun(self):
rank=09 L15: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py",
line 128, in irun
rank=09 L16: self.atoms.get_forces()
rank=09 L17: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/atoms.py",
line 791, in get_forces
rank=09 L18: forces = self._calc.get_forces(self)
rank=09 L19: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/abc.py",
line 23, in get_forces
rank=09 L20: return self.get_property('forces', atoms)
rank=09 L21: File
"/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/site-packages/ase-3.21.0b1-py3.8.egg/ase/calculators/calculator.py",
line 736, in get_property
rank=09 L22: self.calculate(atoms, [name], system_changes)
rank=09 L23: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 322, in calculate
rank=09 L24: for _ in self.icalculate(atoms, properties,
system_changes):
rank=09 L25: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 345, in icalculate
rank=09 L26: self.set_positions(atoms)
rank=09 L27: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/calculator.py",
line 545, in set_positions
rank=09 L28: nlcao, nrand = self.wfs.initialize(self.density,
self.hamiltonian,
rank=09 L29: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/wavefunctions/fdpw.py",
line 307, in initialize
rank=09 L30: hamiltonian.update(density)
rank=09 L31: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 232, in update
rank=09 L32: atomic_energies = self.update_corrections(density, W_aL)
rank=09 L33: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hamiltonian.py",
line 290, in update_corrections
rank=09 L34: eU, dHU_sp = hubbard(setup, D_sp)
rank=09 L35: File
"/scratch/apps/gpaw/20.1/gcc/8.3.0/lib/python3.8/site-packages/gpaw/hubbard.py",
line 13, in hubbard
rank=09 L36: nn = (2 * np.array(l_j) + 1)[0:nl[0]].sum()
rank=09 L37: IndexError: index 0 is out of bounds for axis 0 with size 0
GPAW CLEANUP (node 9): <class 'IndexError'> occurred. Calling MPI_Abort!
Rank 7 [Mon Sep 30 18:25:22 2024] [c1-0c0s14n0] application called
MPI_Abort(MPI_COMM_WORLD, 42) - process 7
Rank 8 [Mon Sep 30 18:25:22 2024] [c1-0c0s14n0] application called
MPI_Abort(MPI_COMM_WORLD, 42) - process 8
Rank 6 [Mon Sep 30 18:25:22 2024] [c1-0c0s14n0] application called
MPI_Abort(MPI_COMM_WORLD, 42) - process 6
Rank 9 [Mon Sep 30 18:25:22 2024] [c1-0c0s14n0] application called
MPI_Abort(MPI_COMM_WORLD, 42) - process 9
_pmiu_daemon(SIGCHLD): [NID 00248] [c1-0c0s14n0] [Mon Sep 30 18:25:22 2024]
PE RANK 8 exit signal Aborted
[NID 00248] 2024-09-30 18:25:22 Apid 24728226: initiated application
termination
Application 24728226 exit codes: 134
Application 24728226 resources: utime ~6s, stime ~2s, Rss ~218192, inblocks
~734, outblocks ~0
I want to emphasize that the paw setup I'm using for La was downloaded from
an older version of tar files available at the GPAW site. In my output
file, I noticed that the valence state of La doesn't include the f-orbital.
Here's the La setup from my output file.
La-setup:
name: Lanthanum
id: 9392f4749781b696b062ab610be201f0
Z: 57.0
valence: 11
core: 46
charge: 0.0
Hubbard U: 3.400000 eV (l=3, scale=True)
file: /home/fuelcells_batteries/14i170002/gpaw-setups-0.9.20000/La.PBE.gz
compensation charges: gauss, rc=0.32, lmax=2
cutoffs: 2.14(filt), 2.20(core),
valence states:
energy radius
5s(2.00) -38.887 1.217
6s(2.00) -3.677 1.217
5p(6.00) -22.409 1.058
5d(1.00) -3.094 1.005
*p 4.803 1.058
*d 24.118 1.005
Is that the reason I am getting the error message? But why index error?
Best regards
Punit
On Mon, 30 Sept 2024 at 11:43, Jens Jørgen Mortensen <jjmo at dtu.dk> wrote:
> Can you show a bit more of the error message? Perhaps everything from
> rank=11.
>
> Jens Jørgen
>
> Den 28.09.2024 kl. 15.44 skrev Punit Kumar via gpaw-users:
> > Dear users,
> >
> > I need assistance related to Hubbard U correction implementation in
> > GPAW. I want to include Hubbard U for the f-orbital of La and the d-
> > orbital of Fe for the LaFeO3 material. But, when I ran the calculation,
> > an index error occurred. A snapshot of the error is mentioned below:
> >
> > GPAW CLEANUP (node 13): <class 'IndexError'> occurred. Calling
> MPI_Abort!
> > rank=11 L09: File "ucf.py", line 36, in <module>
> > rank=10 L39: IndexError: index 0 is out of bounds for axis 0 with size 0
> > rank=11 L10: opt.run(fmax=0.1)
> > rank=11 L11: File "/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/
> > site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py", line
> > 275, in run
> > GPAW CLEANUP (node 12): <class 'IndexError'> occurred. Calling
> MPI_Abort!
> > rank=11 L12: return Dynamics.run(self)
> > rank=11 L13: File "/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/
> > site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py", line
> > 162, in run
> > rank=11 L14: for converged in Dynamics.irun(self):
> > rank=11 L15: File "/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/
> > site-packages/ase-3.21.0b1-py3.8.egg/ase/optimize/optimize.py", line
> > 128, in irun
> > rank=11 L16: self.atoms.get_forces()
> > rank=11 L17: File "/scratch/apps/ase/3.19.0/gcc/8.3.0/lib/python3.8/
> > site-packages/ase-3.21.0b1-py3.8.egg/ase/constraints.py", line 2420, in
> > get_forces
> > rank=11 L18: stress = self.atoms.get_stress(**kwargs)
> >
> > I want to mention that when I remove the Hubbard correction for the La
> > f-orbital, the calculation runs without error. However, when I include
> > the La f-orbital, it gives me an index error. I have attached my input
> > file below, and my calculation setup is mentioned as follows:
> >
> > from ase.io <http://ase.io> import *
> > from ase.spacegroup import *
> > from ase.optimize import *
> > from ase.constraints import *
> > from gpaw import GPAW, PW, FermiDirac, MixerSum, Mixer
> > from ase.visualize import view
> >
> > # structure of lfo
> > lfo = read('initial.traj')
> >
> > calc = GPAW(mode=PW(450),
> > xc='PBE',
> > spinpol=True,
> > nbands='nao',
> > kpts={'size':(4,4,3),'gamma':True},
> > eigensolver='dav',
> > setups={'Fe': ':d,5.16', 'La': ':f,3.40'},
> > mixer=MixerSum(0.05, 5, 100),
> > maxiter=1000,
> > occupations=FermiDirac(0.1,fixmagmom=False),
> > symmetry={'point_group':False},
> > convergence={'energy': 1.0e-4, 'density': 1.0e-5},
> > txt='lfo.out')
> >
> > lfo.set_calculator(calc)
> > calc.attach(calc.write, 10, 'lfo.gpw', mode='all')
> >
> > ucf = UnitCellFilter(lfo, [True,True,True,True,True,True])
> > opt = BFGS(ucf, logfile='opt.log')
> > traj = Trajectory('lfo.traj', 'w', lfo)
> > opt.attach(traj)
> > opt.run(fmax=0.1)
> >
> > Can anyone help me resolve this issue?
> >
> > Best regards
> > Punit
> >
> >
> >
> >
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
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