Add 2.2.1 (#113)

* add ff files * add draft version * Update README * Do not assume `canary` is a module * print actual error * could it be flaky conformer gen? minimize first? * Lint --------- Co-authored-by: Matthew W. Thompson <[email protected]>
openforcefield · Sep 12, 2024 · 3fabe58 · 3fabe58
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # OpenFF Force Fields
 
-[![Build Status](https://github.com/openforcefield/openff-forcefields/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amaster+workflow%3ACI)
+[![Build Status](https://github.com/openforcefield/openff-forcefields/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amain+workflow%3ACI)
 
 
 This repository contains force fields released by the [Open Force Field Initiative](https://openforcefield.org).
@@ -28,6 +28,8 @@ Details for each force field in this repository can be found in the following ta
 
 | Filename                                    | DOI                                                                                                       | FF line | Release Date  | Major format changes? |
 |---------------------------------------------|-----------------------------------------------------------------------------------------------------------|---------|---------------|-----------------------|
+| `openff-2.2.1.offxml`                   |                                                                                                           | Sage    | September 11, 2024 | No                    |
+| `openff_unconstrained-2.2.1.offxml`     |                                                                                                           | Sage    | September 11, 2024 | No                    |
 | `openff-2.2.1-rc1.offxml`                   |                                                                                                           | Sage    | July 22, 2024 | No                    |
 | `openff_unconstrained-2.2.1-rc1.offxml`     |                                                                                                           | Sage    | July 22, 2024 | No                    |
 | `openff-2.2.0.offxml`                       | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10995191.svg)](https://doi.org/10.5281/zenodo.10995191) | Sage    | April 18, 2024 | No                    |
@@ -177,6 +179,8 @@ Force fields moving forward will be called `name-X.Y.Z`
 
 - `2024.07.0`: This release adds `openff-2.2.1-rc1.offxml` and `openff_unconstrained-2.2.1-rc1.offxml`, which contains re-fit valence parameters where linear angles have been pinned to linear equilibrium values.
 
+- `2024.09.0` This release adds the Sage 2.2.1 force field with `openff-2.2.1.offxml` and `openff_unconstrained-2.2.1.offxml`, with identifical parameters to 2.2.1-rc1.
+
 #### Acknowledgements
 
 Project based on the

diff --git a/canary/scripts/test_hmr.py b/canary/scripts/test_hmr.py
@@ -1,13 +1,13 @@
-import importlib.resources
+import pathlib
 import sys
 
 import numpy as np
 import openmm.app
 import openmm.unit
-from openff.toolkit.topology import Molecule
+from openff.toolkit import ForceField, Molecule
 from openmmforcefields.generators import SystemGenerator
 
-DATA_PATH = importlib.resources.files("canary") / "data"
+DATA_PATH = pathlib.Path(".") / "canary" / "data"
 coverage_mols = DATA_PATH / "coverage.smi"
 propyne_mols = DATA_PATH / "propynes.smi"
 
@@ -58,8 +58,13 @@ def hmr_driver(mol, ff_name):
 
     integrator = openmm.LangevinMiddleIntegrator(temperature, collision_rate, timestep)
     context = openmm.Context(system, integrator)
+
+    # generate conformers, minimize, and set positions
     mol.generate_conformers(n_conformers=1)
-    context.setPositions(mol.conformers[0].to_openmm())
+    ff = ForceField(f"{ff_name}.offxml")
+    ic = ff.create_interchange(mol.to_topology())
+    ic.minimize()
+    context.setPositions(ic.positions.to_openmm())
 
     # Run for 10 ps
     integrator.step(2500)
@@ -73,7 +78,7 @@ def hmr_driver(mol, ff_name):
 
 if __name__ == "__main__":
     """This function expects to be called with a list of OFFXML files passed to it,
-    i.e. piped from git diff upstream/master  --name-only"""
+    i.e. piped from git diff upstream/main --name-only"""
     # Read force field filenames from stdin
     failed_runs = []
     for line in sys.stdin:
@@ -98,11 +103,12 @@ def hmr_driver(mol, ff_name):
             except NANEnergyError:
                 failed_runs.append([mol.to_smiles(), ff_name, "NaN energy"])
 
-            except Exception:
+            except Exception as e:
                 # OpenMM's OpenMMException cannot be caught as it does not
                 # inherit from BaseException; therefore this clause may
                 # hit other errors than NaN positions
-                failed_runs.append([mol.to_smiles(), ff_name, "NaN position(s)"])
+                # failed_runs.append([mol.to_smiles(), ff_name, "NaN position(s)"])
+                failed_runs.append([mol.to_smiles(), ff_name, str(e)])
 
     if len(failed_runs) > 0:
         raise HMRCanaryError("HMR tests failed:", failed_runs)