search

hackingmaterials / atomate

atomate is a powerful software for computational materials science and contains pre-built workflows.
https://hackingmaterials.github.io/atomate
Other
245 stars 175 forks source link

numpy.bool_ error #792

Open jinlhr542 opened 2 months ago

jinlhr542 commented 2 months ago 
# Create a bandstructure from the workflow from the atomate presets
import numpy as np
from pymatgen.core import Structure
from fireworks import LaunchPad
from atomate.vasp.workflows.presets.core import wf_bandstructure
from atomate.vasp.powerups import add_modify_incar

# load structure from file
struct = Structure.from_file('POSCAR')  # note: many file formats supported, see function docs

# create the Workflow
wf = wf_bandstructure(struct)

# finally, instatiate the LaunchPad and add the workflow to it
lpad = LaunchPad.auto_load() # loads this based on the FireWorks configuration
lpad.add_wf(wf)

(3.12) [xys@master test]$ python test.py Traceback (most recent call last): File "/home/xys/test/test.py", line 15, in lpad.add_wf(wf) File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/fireworks/core/launchpad.py", line 399, in add_wf self.workflows.insert_one(wf.to_db_dict()) File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/collection.py", line 658, in insert_one self._insert_one( File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/collection.py", line 598, in _insert_one self.__database.client._retryable_write( File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/mongo_client.py", line 1575, in _retryable_write return self._retry_with_session(retryable, func, s, bulk, operation, operation_id) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/mongo_client.py", line 1461, in _retry_with_session return self._retry_internal( ^^^^^^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/_csot.py", line 108, in csot_wrapper return func(self, *args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/mongo_client.py", line 1507, in _retry_internal ).run() ^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/mongo_client.py", line 2353, in run return self._read() if self._is_read else self._write() ^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/mongo_client.py", line 2470, in _write return self._func(self._session, conn, self._retryable) # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/collection.py", line 586, in _insert_command result = conn.command( ^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/helpers.py", line 342, in inner return func(args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/pool.py", line 1017, in command self._raise_connection_failure(error) File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/pool.py", line 989, in command return command( ^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/network.py", line 152, in command request_id, msg, size, max_doc_size = message._op_msg( ^^^^^^^^^^^^^^^^ File "/home/xys/miniconda3/envs/3.12/lib/python3.12/site-packages/pymongo/message.py", line 758, in _op_msg return _op_msguncompressed(flags, command, identifier, docs, opts) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bson.errors.InvalidDocument: cannot encode object: True, of type: <class 'numpy.bool'>