Hi Developers,
I am trying to run the aiida-vibroscopy code. I got the error I guess it did not recognize the pseudopotential. I have pseudo potential label installed as pbe_psp. I am using overrides.yaml (please see the inputs below). Can you please help me fix this issue?
Best
Rijan
(aiidaENV) rkarkee@ch-fe1:/lustre/scratch5/rkarkee> python submit_with_overrides.py
Traceback (most recent call last):
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida_quantumespresso/workflows/pw/base.py”, line 161, in get_builder_from_protocol
pseudo_family = orm.QueryBuilder().append(pseudo_set, filters={‘label’: pseudo_family}).one()[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida/orm/querybuilder.py”, line 1105, in one
raise NotExistent(‘No result was found’)
aiida.common.exceptions.NotExistent: No result was found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/lustre/scratch5/.mdt0/rkarkee/submit_with_overrides.py”, line 85, in
main()
File “/lustre/scratch5/.mdt0/rkarkee/submit_with_overrides.py”, line 49, in main
builder = IRamanSpectraWorkChain.get_builder_from_protocol(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida_vibroscopy/workflows/spectra/iraman.py”, line 113, in get_builder_from_protocol
phonon = PhononWorkChain.get_builder_from_protocol(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida_vibroscopy/workflows/phonons/base.py”, line 258, in get_builder_from_protocol
scf = PwBaseWorkChain.get_builder_from_protocol(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida_quantumespresso/workflows/pw/base.py”, line 163, in get_builder_from_protocol
raise ValueError(
ValueError: required pseudo family SSSP/1.3/PBEsol/efficiency
is not installed. Please use aiida-pseudo install
toinstall it.
%%%%%%%%%%%%%
overrides.yaml
%%%%%%%%%%%%%%%%%%%%%%%%
clean_workdir: false # whether to clean the working directiories
dielectric:
clean_workdir: false
kpoints_parallel_distance: 0.2 # kpoints distance in Angstrom^-1 to sample the BZ parallel to the electric field. If used, it should help in converging faster the final results
property: raman
central_difference: # if you know what you are doing, custom numerical derivatives with respect to electric field
accuracy: 2
electric_field_step: 0.0005
scf:
kpoints_distance: 0.4 # kpoints distance in Angstrom^-1 to sample the BZ
kpoints_force_parity: false
max_iterations: 5
pw:
metadata:
options:
max_wallclock_seconds: 43200
resources:
num_machines: 1
num_mpiprocs_per_machine: 256
queue_name: standard # for SLURM
# account: account_name # for SLURM, also for project etc
withmpi: true
parameters:
ELECTRONS:
conv_thr: 2.0e-10
electron_maxstep: 100
mixing_beta: 0.2
SYSTEM:
ecutrho: 280.0
ecutwfc: 70.0
vdw_corr: Grimme-D2
settings:
sleep_submission_time: 1.0
phonon:
clean_workdir: false
displacement_generator:
distance: 0.01 # atomic displacements for phonon calculation, in Angstrom
scf:
kpoints_distance: 0.15 # kpoints distance in Angstrom^-1 to sample the BZ
kpoints_force_parity: false
max_iterations: 5
pw:
metadata:
options:
max_wallclock_seconds: 43200
resources:
num_machines: 1
num_mpiprocs_per_machine: 1
# queue_name: partition_name # for SLURM
# account: account_name # for SLURM, also for project etc
withmpi: true
settings:
cmdline: [‘-nk’, ‘8’]
# gamma_only: True # to use only if KpointsData has only a mesh 1 1 1 0 0 0 (i.e. Gamma not shifted)
parameters:
ELECTRONS:
conv_thr: 2.0e-12
electron_maxstep: 80
mixing_beta: 0.4
SYSTEM:
ecutwfc: 70.0
vdw_corr: Grimme-D2
settings:
sleep_submission_time: 1.0 # waiting time in seconds between different submission of SCF calculation. Recommended to be at least 1 second, to not overload.
settings:
run_parallel: true
use_primitive_cell: false
symmetry:
distinguish_kinds: false
is_symmetry: true
symprec: 1.0e-05
%%%%%%%%%%%%%%%%%%
submit.py
%%%%%%%%%%%%%%%%%%%%%
-- coding: utf-8 --
pylint: disable=line-too-long,wildcard-import,pointless-string-statement,unused-wildcard-import
“”“Submit an IRamanSpectraWorkChain via the get_builder_from_protocol using the overrides.”“”
from pathlib import Path
from aiida import load_profile
from aiida.engine import submit
from aiida.orm import *
from aiida_quantumespresso.common.types import ElectronicType
from aiida_vibroscopy.workflows.spectra.iraman import IRamanSpectraWorkChain
load_profile()
=============================== INPUTS ===============================
Please, change the following inputs.
mesh = [[4, 4, 2], [0.5, 0.5, 0.5]]
pseudo_family_name=‘pbe_psp’
pw_code_label = ‘qe-7.3@newhpc’
structure_id = 21 # PK or UUID of your AiiDA StructureData
protocol = ‘fast’ # also ‘moderate’ and ‘precise’; ‘moderate’ should be good enough in general
overrides_filepath = ‘./overrides.yaml’ # should be a path, e.g. /path/to/overrides.yaml. Format is YAML