add qcmanybody interface

[loriab]

There's a project https://github.com/molSSI/QCmanybody for serving up BSSE corrections and MBE truncations. As it's integrated with QCEngine and has a nice schema interface, it's pretty easy to extend to optimizations with geomeTRIC, so here's some proposed changes. It'll require QCManyBody v0.3.0 and QCEngine v0.30.0 (neither of which are minted yet) and any QCEngine program harness that can do ghost atoms (Psi4, NWChem, Cfour known to work; GAMESS cannot).

Glad to answer any questions or make changes.

[leeping]

I assume this is a better way to get the name of the test folder? Please confirm.

[loriab]

Yes, function.__name__ gets the name of the test function (e.g., test_lif_bsse) but node.name gets the per-test name that includes parametrization (e.g., test_lif_bsse[psi4-nocp]). The previous function way was no trouble when the tests were run in serial, but it led to file overwriting when running pytest in parallel.

[leeping]

I don't think geomeTRIC has a NWChem interface, but maybe that's okay if the intent is for QCEngine to call NWChem.

[loriab]

Right, integrating QCManyBody for geomeTRIC's first-class engines is a separate project (and one I didn't even think of initially). This PR is purely so that geometric.run_json can take the slightly different schema layout for an OptimizationInput holding an ordinary gradient specification vs. holding a many-body gradient specification. (The divergence isn't long-term; we're revising the schema.) So the PR is really only good for the run_json half of the QCEngine engine of geomeTRIC.

[leeping]

Have you confirmed that these tests can run locally? How long do the tests take?

[loriab]

Yes, it's not much proof but see below. They take about a minute in parallel (and ordinarily one wouldn't have psi4, nwchem, and cfour all accessible). At the moment they need software versions that are unreleased.

> pytest -v geometric/tests/test_qcengine.py -n 8
================================================================= test session starts ==================================================================
platform linux -- Python 3.12.2, pytest-8.1.1, pluggy-1.4.0 -- /psi/toolchainconda/envs/qcmb312_pyd1/bin/python3.12
cachedir: .pytest_cache
rootdir: /psi/gits/geomeTRIC
configfile: pytest.ini
plugins: xdist-3.5.0, typeguard-4.2.1
8 workers [7 items]     
scheduling tests via LoadScheduling

geometric/tests/test_qcengine.py::test_lif_bsse[cfour-nocp] 
geometric/tests/test_qcengine.py::test_lif_bsse[nwchem-cp] 
geometric/tests/test_qcengine.py::test_rdkit_simple 
geometric/tests/test_qcengine.py::test_lif_bsse[psi4-cp] 
geometric/tests/test_qcengine.py::test_lif_bsse[nwchem-nocp] 
geometric/tests/test_qcengine.py::test_lif_bsse[psi4-nocp] 
geometric/tests/test_qcengine.py::test_lif_bsse[cfour-cp] 
[gw0] [ 14%] PASSED geometric/tests/test_qcengine.py::test_rdkit_simple 
[gw3] [ 28%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[cfour-nocp] 
[gw4] [ 42%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[cfour-cp] 
[gw1] [ 57%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[psi4-nocp] 
[gw2] [ 71%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[psi4-cp] 
[gw5] [ 85%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[nwchem-nocp] 
[gw6] [100%] PASSED geometric/tests/test_qcengine.py::test_lif_bsse[nwchem-cp] 

=================================================================== warnings summary ===================================================================
  /psi/gits/geomeTRIC/geometric/tests/addons.py:51: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import parse_version

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================================= 7 passed, 8 warnings in 68.03s (0:01:08) =======================================================

[leeping]

Hi Lori,

Thanks a lot for the contribution! Does QCManyBody automate the calls to Psi4, NWChem, Cfour to perform the single-point calculations needed for BSSE and MBE? That sounds very useful.

I'm happy for this to become a part of the main branch but I'd like to ensure the tests can run on my local machine before I do that, so we can wait for the right versions of the MolSSI packages to be released first. What do you think?

• Lee-Ping

[loriab]

Thanks a lot for the contribution! Does QCManyBody automate the calls to Psi4, NWChem, Cfour to perform the single-point calculations needed for BSSE and MBE? That sounds very useful.

You're welcome, thanks for taking a look! QCManyBody has two interfaces. So, yes, for the high level intf, you feed it a schema instance, and it toddles off to QCEngine and runs all the NWChem, Psi4, etc. gradients in serial for each of the subfragments the job needs, then returns to caller a schema with the summed-up many-body gradient. Or there's a low-level intf that supplies an iterator over needed subsystems/model chems, then you run the jobs, collect energies/gradients into a data structure, and hand that back to qcmanybody to sum up. Example for energies here. Dependencies are numpy and qcelemental. Glad to talk further if this would be useful to you.

I'm happy for this to become a part of the main branch but I'd like to ensure the tests can run on my local machine before I do that, so we can wait for the right versions of the MolSSI packages to be released first. What do you think?

Sure, perfectly fine. I should get the next QCManyBody release out today, but QCEngine may be a couple weeks. I'll ping this thread when the tests are actually runable :-)