"TypeError: 'NoneType' object is not subscriptable" in harmonic phonon calculation

[minnie178]

Hi all,

I am doing the SSCHA minimization for silicon. The relax calculation has converged, and I was proceeding for the harmonic phonon calculation, and came across the error 'TypeError: 'NoneType' object is not subscriptable' during the phonon calculation using finite displacement approach. I am using quantum espresso calculator. The error comes up during the execution of the command
si_harmonic_dyn = CC.Phonons.compute_phonons_finite_displacements (si_structure_relaxed, calculator, supercell = (2,2,2)

The input python script is enclosed.

import sscha, sscha.Ensemble, sscha.SchaMinimizer
import sscha.Relax, sscha.Utilities
import cellconstructor as CC, cellconstructor.Phonons
import cellconstructor.Structure, cellconstructor.calculators
from cellconstructor.calculators import Espresso
import numpy as np, matplotlib.pyplot as plt
import sys, os
pseudos = {"Si": "Si.pbe-n-kjpaw_psl.1.0.0.UPF"}
input_params = { "control": {"calculation" :'relax',
"pseudo_dir" : "pseudos",
"tprnfor" : True,
"tstress" : True,
},
"system": {"ecutwfc" : 45,
"ecutrho" : 180,
"nat" : 4,
"ntyp" : 1,
"degauss" : 0.02,
"occupations" : 'smearing',
"smearing" : 'mv'
},
"electrons": {"conv_thr": 8e-10
},
"ions": {"ion_dynamics" : "bfgs"}
}`

`si_structure = CC.Structure.Structure()
si_structure.read_generic_file("Si.cif")
calculator = Espresso(input_data = input_params, pseudopotentials = pseudos) #, kspacing = 'k_spacing')
relax = CC.calculators.Relax(si_structure, calculator)
si_structure_relaxed = relax.static_relax()
si_harmonic_dyn = CC.Phonons.compute_phonons_finite_displacements (si_structure_relaxed, calculator, supercell = (2,2,2))
si_harmonic_dyn.Symmetrize()
si_harmonic_dyn.save_qe("harmonic_dyn")
si_harmonic_dyn.ForcePositiveDefinite()
TEMPERATURE = 300
N_CONFIGS = 50
MAX_ITERATIONS = 20
ensemble = sscha.Ensemble.Ensemble(si_harmonic_dyn, TEMPERATURE)
minim = sscha.SchaMinimizer.SSCHA_Minimizer(ensemble)
minim.set_minimization_step(0.01)
relax = sscha.Relax.SSCHA(minim, calculator, N_configs = N_CONFIGS,
max_pop = MAX_ITERATIONS)
ioinfo = sscha.Utilities.IOInfo()
ioinfo.SetupSaving("minim_info")
relax.setup_custom_functions(custom_function_post = ioinfo.CFP_SaveAll)
relax.relax(get_stress = True)
relax.minim.finalize()
relax.minim.dyn.save_qe("sscha_T{}_dyn".format(TEMPERATURE))

Any help on this is greatly appreciated. Thanks in advance!

[mesonepigreco]

Hi, could you paste here the complete error stack? Otherwise it is difficult to see how it emerges

[minnie178]

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

---

TypeError Traceback (most recent call last)
Cell In[12], line 1
----> 1 si_harmonic_dyn = CC.Phonons.compute_phonons_finite_displacements (si_structure_relaxed, calculator, supercell = (2,2,2))

File ~/.local/lib/python3.10/site-packages/cellconstructor/Phonons.py:4498, in compute_phonons_finite_displacements(structure, ase_calculator, epsilon, supercell, progress, progress_bar, use_symmetries, debug)
4496 if not SPGLIB:
4497 raise ImportError("SPGLIB is not installed. Cannot use symmetries. Rerun this subroutine with use_symmetries = False")
-> 4498 return compute_phonons_finite_displacements_sym(structure, ase_calculator, epsilon,
4499 supercell, progress, progress_bar, debug=debug)
4501 super_structure = structure.generate_supercell(supercell)
4502 final_dyn = Phonons(super_structure)

File ~/.local/lib/python3.10/site-packages/cellconstructor/Phonons.py:4746, in compute_phonons_finite_displacements_sym(structure, ase_calculator, epsilon, supercell, progress, progress_bar, debug, timer)
4744 fc = timer.execute_timed_function(Settings.GoParallel, compute_force, list_of_calculations, reduce_op='+')
4745 else:
-> 4746 fc = Settings.GoParallel(compute_force, list_of_calculations, reduce_op='+')
4748 #if Settings.am_i_the_master():
4749 # np.savetxt("FC_before_subtraction.dat", fc)
4751 energy = None

File ~/.local/lib/python3.10/site-packages/cellconstructor/Settings.py:283, in GoParallel(function, list_of_inputs, reduce_op, timer)
281 result = 0
282 for x in computing_list:
--> 283 result += function(x, **kwargs)
284 elif reduce_op == "*":
285 result = 1

File ~/.local/lib/python3.10/site-packages/cellconstructor/Phonons.py:4734, in compute_phonons_finite_displacements_sym..compute_force(indices)
4732 ase_calculator.set_label("disp_{}".format(3i + j))
4733 ase_calculator.directory = "disp_{}".format(3i + j)
-> 4734 energy, forces = calculators.get_energy_forces(ase_calculator, s)
4735 fc_tmp = np.zeros((nat3, nat3), dtype = np.double)
4736 fc_tmp[3*i+j,:] -= forces.ravel()

File ~/.local/lib/python3.10/site-packages/cellconstructor/calculators.py:65, in get_energy_forces(calculator, structure)
63 elif isinstance(calculator, Calculator):
64 calculator.calculate(structure)
---> 65 return calculator.results["energy"], calculator.results["forces"]
66 else:
67 raise ValueError("Error, unknown calculator type")

TypeError: 'NoneType' object is not subscriptable

[mesonepigreco]

This seems a problem with the espresso calculator.
However, it is strongly suggested to use ph.x from quantum espresso to evaluate the harmonic dynamical matrix, this has the same output that can be directly read by the SSCHA.
Computing the phonons directly with the finite displacement approach implemented within the SSCHA is suited for fast force-fields, for DFT calculation is much quicker to just run DFPT via quantum espresso.

The same holds for the complete SSCHA minimization; it is suggested to use a remote cluster submission (as explained in Tutorial 2), as the ASE calculator is extremely slow and not well-suited for performing parallel calculations, especially on a cluster.

[minnie178]

Thanks a lot for your suggestions.