Merge pull request #946 from openforcefield/3fad

Support GROMACS's `3fad` virtual sites

openff/interchange/_tests/conftest.py

@@ -66,8 +66,27 @@ def sage_with_planar_monovalent_carbonyl(sage):
             outOfPlaneAngle=Quantity("0 * degree ** 1"),
             inPlaneAngle=Quantity("120 * degree ** 1"),
             charge_increment1="0.1 * elementary_charge ** 1",
-            charge_increment2="0.1 * elementary_charge ** 1",
-            charge_increment3="0.1 * elementary_charge ** 1",
+            charge_increment2="0.0 * elementary_charge ** 1",
+            charge_increment3="0.0 * elementary_charge ** 1",
+        ),
+    )
+
+    return sage
+
+
+@pytest.fixture
+def sage_with_sigma_hole(sage):
+    """Fixture that loads an SMIRNOFF XML with a C-Cl sigma hole."""
+    sage.get_parameter_handler("VirtualSites")
+    sage["VirtualSites"].add_parameter(
+        parameter=VirtualSiteType(
+            name="EP",
+            smirks="[#6:1]-[#17:2]",
+            distance=1.4 * unit.angstrom,
+            type="BondCharge",
+            match="once",
+            charge_increment1=0.1 * unit.elementary_charge,
+            charge_increment2=0.2 * unit.elementary_charge,
         ),
     )
 

openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py

@@ -4,9 +4,8 @@
 import numpy
 import parmed
 import pytest
-from openff.toolkit import ForceField, Molecule, Topology
+from openff.toolkit import ForceField, Molecule, Quantity, Topology, unit
 from openff.toolkit.typing.engines.smirnoff import VirtualSiteHandler
-from openff.units import unit
 from openff.units.openmm import ensure_quantity
 from openff.utilities import (
     get_data_file_path,
@@ -24,11 +23,7 @@
 from openff.interchange.components.nonbonded import BuckinghamvdWCollection
 from openff.interchange.components.potentials import Potential
 from openff.interchange.drivers import get_gromacs_energies, get_openmm_energies
-from openff.interchange.exceptions import (
-    GMXMdrunError,
-    UnsupportedExportError,
-    VirtualSiteTypeNotImplementedError,
-)
+from openff.interchange.exceptions import GMXMdrunError, UnsupportedExportError
 from openff.interchange.interop.gromacs._import._import import (
     _read_box,
     _read_coordinates,
@@ -76,9 +71,12 @@ def test_tip4p_dimer(self, tip4p, water_dimer):
 @skip_if_missing("openmm")
 @needs_gmx
 class TestGROMACSGROFile:
-    _INTERMOL_PATH = resources.files(
-        "intermol.tests.gromacs.unit_tests",
-    )
+    try:
+        _INTERMOL_PATH = resources.files(
+            "intermol.tests.gromacs.unit_tests",
+        )
+    except ModuleNotFoundError:
+        _INTERMOL_PATH = None
 
     @skip_if_missing("intermol")
     def test_load_gro(self):
@@ -499,7 +497,6 @@ def test_common_boxes(self, pdb_file):
 
 
 @needs_gmx
-@pytest.mark.skip("Needs rewrite")
 class TestGROMACSVirtualSites:
     @pytest.fixture
     def sigma_hole_type(self, sage):
@@ -558,23 +555,19 @@ def test_sigma_hole_example(self, sage_with_sigma_hole):
 
         assert abs(numpy.sum([p.charge for p in gmx_top.atoms])) < 1e-3
 
-    def test_carbonyl_example(self, sage_with_monovalent_lone_pair):
-        """Test that a single-molecule DivalentLonePair example runs"""
-        mol = MoleculeWithConformer.from_smiles("C=O", name="Carbon_monoxide")
+    def test_carbonyl_example(self, sage_with_planar_monovalent_carbonyl, ethanol):
+        """Test that a single-molecule planar carbonyl example can run 0 steps."""
+        ethanol.generate_conformers(n_conformers=1)
 
-        out = Interchange.from_smirnoff(
-            force_field=sage_with_monovalent_lone_pair,
-            topology=mol.to_topology(),
-        )
-        out.box = [4, 4, 4]
-        out.positions = mol.conformers[0]
+        hexanal = MoleculeWithConformer.from_smiles("CCCCCC=O")
+        hexanal._conformers[0] += Quantity("2 nanometer")
 
-        with pytest.raises(
-            VirtualSiteTypeNotImplementedError,
-            match="MonovalentLonePair not implemented.",
-        ):
-            # TODO: Sanity-check reported energies
-            get_gromacs_energies(out)
+        topology = Topology.from_molecules([ethanol, hexanal])
+        topology.box_vectors = Quantity([4, 4, 4], "nanometer")
+
+        get_gromacs_energies(
+            sage_with_planar_monovalent_carbonyl.create_interchange(topology),
+        )
 
     @skip_if_missing("openmm")
     def test_tip4p_charge_neutrality(self, tip4p, water_dimer):

openff/interchange/interop/gromacs/export/_export.py

@@ -10,6 +10,7 @@
     GROMACSSystem,
     GROMACSVirtualSite2,
     GROMACSVirtualSite3,
+    GROMACSVirtualSite3fad,
     LennardJonesAtomType,
     PeriodicImproperDihedral,
     PeriodicProperDihedral,
@@ -247,6 +248,20 @@ def _write_virtual_sites(self, top, molecule_type):
                     "\n",
                 )
 
+            elif isinstance(gromacs_virtual_site, GROMACSVirtualSite3fad):
+                top.write("[ virtual_sites3 ]\n")
+                top.write("; parent, orientation atoms, func, theta, d\n")
+                top.write(
+                    f"{gromacs_virtual_site.site}\t"
+                    f"{gromacs_virtual_site.orientation_atoms[0]}\t"
+                    f"{gromacs_virtual_site.orientation_atoms[1]}\t"
+                    f"{gromacs_virtual_site.orientation_atoms[2]}\t"
+                    f"{gromacs_virtual_site.func}\t"
+                    f"{gromacs_virtual_site.theta}\t"
+                    f"{gromacs_virtual_site.d}\t"
+                    "\n",
+                )
+
             else:
                 raise NotImplementedError()
 

openff/interchange/interop/gromacs/export/_virtual_sites.py

@@ -11,11 +11,13 @@
     GROMACSVirtualSite,
     GROMACSVirtualSite2,
     GROMACSVirtualSite3,
+    GROMACSVirtualSite3fad,
 )
 from openff.interchange.models import VirtualSiteKey
 from openff.interchange.smirnoff._virtual_sites import (
     _BondChargeVirtualSite,
     _DivalentLonePairVirtualSite,
+    _MonovalentLonePairVirtualSite,
     _VirtualSite,
 )
 
@@ -26,10 +28,20 @@ def _create_gromacs_virtual_site(
     virtual_site_key: VirtualSiteKey,
     particle_map: dict[int | VirtualSiteKey, int],
 ) -> GROMACSVirtualSite:
-    offset = interchange.topology.atom_index(
-        interchange.topology.atom(min(virtual_site_key.orientation_atom_indices)),
+
+    # Orientation atom indices are topology indices, but here they need to be indexed as molecule
+    # indices. Store the difference between an orientation atom's molecule and topology indices.
+    # (It can probably be any of the orientation atoms.)
+    parent_atom = interchange.topology.atom(
+        virtual_site_key.orientation_atom_indices[0],
     )
 
+    # This lookup scales poorly with system size, but it's not clear how to work around the
+    # tool's ~O(N) scaling of topology lookups
+    offset = interchange.topology.atom_index(
+        parent_atom,
+    ) - parent_atom.molecule.atom_index(parent_atom)
+
     # These are GROMACS "molecule" indices, already mapped back from the topology on to the molecule
     gromacs_indices: list[int] = [
         particle_map[openff_index] - offset + 1
@@ -98,4 +110,25 @@ def _create_gromacs_virtual_site(
         else:
             raise NotImplementedError()
 
+    if isinstance(virtual_site, _MonovalentLonePairVirtualSite):
+        if virtual_site.out_of_plane_angle != 0.0:
+            raise NotImplementedError(
+                "Non-zero out-of-plane angles not yet supported in GROMACS export.",
+            )
+
+        # In the plane of three atoms, GROMACS calls this 3fad and gives the example
+        #
+        # [ virtual_sites3 ]
+        # ; Site  from               funct   theta      d
+        # 5       1     2     3      3       120        0.5
+        # https://manual.gromacs.org/current/reference-manual/topologies/particle-type.html
+
+        return GROMACSVirtualSite3fad(
+            name=virtual_site_key.name,
+            site=particle_map[virtual_site_key] - offset + 1,
+            orientation_atoms=gromacs_indices,
+            theta=virtual_site.in_plane_angle.m_as(unit.degree),
+            d=virtual_site.distance.m_as(unit.nanometer),
+        )
+
     raise NotImplementedError()

openff/interchange/interop/gromacs/models/models.py

@@ -57,6 +57,7 @@ class GROMACSAtom(DefaultModel):
     mass: Quantity
 
 
+# Should the physical values (distance/angles) be float or Quantity?
 class GROMACSVirtualSite(DefaultModel):
     """Base class for storing GROMACS virtual sites."""