molssi / mqcas

History information for the data in the MolSSI QCArchive Server (MQCAS)

MQCAS

History information for the data in the MolSSI QCArchive Server (MQCAS)

This repository servers several goals:

• Discuss the MQCAS data and future computational campaigns
• Report issues with the data
• Request additional collections or computations on those collections
• Volunteer compute time for the MQCAS server
• Upload new collections to the MQCAS server

This repository is quite new and needs a substantial infrastructure build out before it can meet these goals. Please check back periodically or open an issue or pull request to help out!

mqcas's Issues

Requesting more functionals for ASCDB.

Hi Matt and Daniel,
Could it be possible to add the two functionals MN15 and wB97M-V to the compute list of the ASCDB database, please?
It would be great to get data with the def2-QZVP basis set, but I understand if it's not possible. :)
Let me know if there is anything I can do.
Thank you,
Pier

ACSDB get_molecules fails

Data Location
Collection ASCDB

Describe the issue
Calling get_molecules() returns an internal server error. This can also be reproduced by querying individual molecules from ASCDB, e.g. client.query_molecules('11757989').

Looking into the logs on molssi10, this might be a slim molecule issue:

[E 200313 10:10:03 web:1788] Uncaught exception GET /molecule (127.0.0.1)
    HTTPServerRequest(protocol='http', host='api.qcarchive.molssi.org', method='GET', uri='/molecule', version='HTTP/1.0', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/dgasmith/miniconda3/envs/qcfprodv13/lib/python3.7/site-packages/tornado/web.py", line 1697, in _execute
        result = method(*self.path_args, **self.path_kwargs)
      File "/home/dgasmith/miniconda3/envs/qcfprodv13/lib/python3.7/site-packages/qcfractal/web_handlers.py", line 238, in get
        molecules = self.storage.get_molecules(**{**body.data.dict(), **body.meta.dict()})
      File "/home/dgasmith/miniconda3/envs/qcfprodv13/lib/python3.7/site-packages/qcfractal/storage_sockets/sqlalchemy_socket.py", line 739, in get_molecules
        data = [Molecule(**d, validate=False, validated=True) for d in rdata]
      File "/home/dgasmith/miniconda3/envs/qcfprodv13/lib/python3.7/site-packages/qcfractal/storage_sockets/sqlalchemy_socket.py", line 739, in <listcomp>
        data = [Molecule(**d, validate=False, validated=True) for d in rdata]
      File "/home/dgasmith/miniconda3/envs/qcfprodv13/lib/python3.7/site-packages/qcelemental/models/molecule.py", line 271, in __init__
        super().__init__(**kwargs)
      File "pydantic/main.py", line 274, in pydantic.main.BaseModel.__init__
    pydantic.error_wrappers.ValidationError: 4 validation errors for Molecule
    masses
      object of type 'NoneType' has no len() (type=type_error)
    real
      object of type 'NoneType' has no len() (type=type_error)
    fragment_charges
      object of type 'NoneType' has no len() (type=type_error)
    fragment_multiplicities
      object of type 'NoneType' has no len() (type=type_error)

Expected behavior
Molecule should be successfully returned.

TensorMol Dataset

Describe the data you'd like
The data associated with the following papers:

• https://pubs.rsc.org/no/content/articlehtml/2018/sc/c7sc04934j
• https://aip.scitation.org/doi/pdf/10.1063/1.5108803

Describe ways to obtain the data
The data needs to be ingested from Q-Chem outputs provided by John Herr. These data are currently in the MSS drive. In order to parse these outputs, we will need to improve qcng's parsers to support geometry optimizations and AIMD.

Willing to contribute
I have time to work on this as part of the MolSSI ML project. John Herr has already contributed the data.

Additional context
We could consider creating an AIMD qcsk structure, but my plan is to ingest AIMD frames as AtomicResults.

S22by5 B2PLYP/adz

Data Location
S22 Dataset

Describe the issue
B2PLYP in the ADZ basis, cp corrected has a massive UE spike indicating one computation is wrong. NoCP does not have this issue.

Additional context

ASCDB needs a tagline

Data Location
ReactionDataset ASCDB

Describe the issue
Its tagline is None.

ASCDB

Describe the data you'd like
Upload the ACCDB dataset found here.

Describe ways to obtain the data
Download data from the ACCDB repository.

Willing to contribute
Pier Morgante should be able to help with the ingestion. MolSSI will help with some compute.

Additional context

Upload Example

import qcportal as ptl
from qcfractal import FractalSnowflake
import pandas as pd

SNOWFLAKE = True

if SNOWFLAKE:
    snowflake = FractalSnowflake()
    client = snowflake.client()
else:
    client = None
print(client)

ds = ptl.collections.ReactionDataset("ASCDB", client=client)

with open("ASCDB.csv", "r") as handle:
    rxns = [x.split(",") for x in handle.read().splitlines()]

gpath = "ASCDB_Geometries"

contrib_name = []
contrib_value = []
for row in rxns[:5]:
    name = row[0]
    rxn = row[1:]

    half = len(rxn) // 2
    molecules = rxn[:half]
    coefs = rxn[half:]

    rxn_data = []
    for mol_name, coef in zip(molecules, coefs):
        mol = ptl.Molecule.from_file(gpath + "/" + mol_name + ".xyz")

        coef = float(coef)
        rxn_data.append((mol, coef))

    rxn = {"default": rxn_data}

    ds.add_rxn(name, rxn)

    contrib_name.append(name)
    contrib_value.append(5)

ds.save()

contrib = {
    "name": "Benchmark",
    "theory_level": "CCSD(T)",
    "values": contrib_value,
    "index": contrib_name,
    "theory_level_details": {"driver": "energy"},
    "units": "hartree",
}
ds.add_contributed_values(contrib)
#ds.save()