Trying to use VASP recipe for the first time

[JohnFengg]

I'm trying to using QUACC package with JOBFLOW wf engine to run a job, my script is like this (got an error before testing if this scripts can work):
####extract the atom objects from database ####
from ase.db import connect
from quacc.recipes.vasp.mp import mp_relax_flow
from quacc.wflow.db import results_to_db

database_path = 'perovskites.db'
db = connect(database_path)

batch_size = 1 #number of structure calculated simultaneously

for i in range(0, 1, batch_size):
structures = db[i:i + batch_size]
flow=mp_relax_flow()
#pre_relax={atoms=structures, preset="MPScanSet", calc_swaps= None, copy_files=None}
results = flow(
structures,
prerelax_job_kwargs=None,
relax_job_kwargs=None,
)

db.close()

when I run the scripts, there is an error:

Traceback (most recent call last):
File "/home/toussaint/high-throughput/model-run.py", line 3, in
from quacc.recipes.vasp.mp import mp_relax_flow
File "/home/toussaint/opt/miniconda3/envs/quacc/lib/python3.10/site-packages/quacc/init.py", line 11, in
from quacc.settings import QuaccSettings
File "/home/toussaint/opt/miniconda3/envs/quacc/lib/python3.10/site-packages/quacc/settings.py", line 22, in
import jobflow
File "/home/toussaint/opt/miniconda3/envs/quacc/lib/python3.10/site-packages/jobflow/init.py", line 14, in
SETTINGS = JobflowSettings()
File "pydantic/env_settings.py", line 40, in pydantic.env_settings.BaseSettings.init
File "pydantic/main.py", line 341, in pydantic.main.BaseModel.init
pydantic.error_wrappers.ValidationError: 1 validation error for JobflowSettings
docs_store
extra fields not permitted (type=value_error.extra)

I have created a jobflow.yaml file and export the path in ~/.bashrc, and it seems like there are no error about the yaml files:

docs_store:
type: MongoStore
host: localhost
port: 27017
database: ase
collection_name: ase
username: toussaint
password: toussaint

I dont know how to fix this, could anyone help me for this?

[Andrew-S-Rosen]

Hi @JohnFengg. Thanks for the report. I'd be happy to help.

The error you are seeing is likely a Pydantic compatibility issue. In short, the entire Materials Project software stack (including Jobflow) transitioned from Pydantic v1 to Pydantic v2 recently. These two versions of Pydantic are not intercomparable.

My assumption is that one of your dependencies is for an older version running on Pydantic v1. Can you please do the following:

1. Report what version of quacc and Jobflow you are using.
2. Update quacc, which will ensure you have the most up-to-date dependencies.

We can debug from there. Also, just as a note, I wish to emphasize that the MP workflows in quacc are merely for demonstration purposes only at the moment. The one true source of MP workflows is in atomate2. I make no guarantees of 1:1 compatibility at the moment, as the MP workflow in atomate2 was only just added the other day, and further validation is needed to ensure they match (for instance, see this PR).

[Andrew-S-Rosen]

That seems like a problem. Let me get that patched and report back shortly.

[Andrew-S-Rosen]

@JohnFengg: It's getting a bit late here so I'll have to fix it tomorrow. I'll ping you when it's patched so you can update your quacc version.

The issue is that the VASP INCAR "co-pilot" routine, which tries to correct INCAR parameters on-the-fly, is changing "efermi" back to "midgap" to abide by the VASP manual. Instead, what we want to do is always respect calc_swaps and assume the user knows what they are doing.

In the meantime, you can do quacc set VASP_INCAR_COPILOT False in the command-line to disable the co-pilot routine so it won't override your changes automatically.

[JohnFengg]

OK, I see. (Get more knowledge about this program :P !) Cant imagine how difficult this work will be for me without your efficient help !
And the command seems a good choice temporarily for me to continute the job.
Good night!!!

[Andrew-S-Rosen]

@JohnFengg: Thanks for your patience. I have patched the issue that was preventing your calc_swaps = {"efermi": None} to register.

A new version of quacc will be minted on PyPI in approximately 10 mins, after which you can do:

pip uninstall quacc
pip install --upgrade quacc

[JohnFengg]

Got it ! @Andrew-S-Rosen Thanks for your supporting. I'll try it later, and now I try to learn how to use theparls and it's indeed easier to understand, thanks for the advise! Keep in touch :p.