add basic rigid body snapshot test

gmso/external/convert_hoomd.py

@@ -284,19 +284,19 @@ def _parse_particle_information(
         site.name if site.atom_type is None else site.atom_type.name
         for site in top.sites
     ]
-    masses = list()
-    charges = list()
-    for site in top.sites:
-        masses.append(
+    masses = np.zeros(len(xyz))
+    charges = np.zeros(len(xyz))
+    for idx, site in enumerate(top.sites):
+        masses[idx] = (
             site.mass.to_value(base_units["mass"])
             if site.mass
             else 1 * base_units["mass"]
         )
-        charges.append(site.charge if site.charge else 0 * u.elementary_charge)
+        charges[idx] = (site.charge if site.charge else 0 * u.elementary_charge)
     # Check for rigid IDs
     rigid_ids = [site.rigid_id for site in top.sites]
     rigid_ids_set = set(rigid_ids)
-    if all(rigid_ids):  # Need to create rigid bodies
+    if None not in rigid_ids:
         n_rigid = len(rigid_ids_set)
         write_rigid = True
     else:
@@ -306,12 +306,14 @@ def _parse_particle_information(
     typeids = np.array([unique_types.index(t) for t in types])
     if write_rigid:
         rigid_masses = np.zeros(n_rigid)
-        rigid_xyz = np.zeros(n_rigid)
+        rigid_xyz = np.zeros((n_rigid, 3))
         # Rigid particle type defaults to "R"; add to front of list
         # TODO: Can we always use "R" here? What if an atom_type is "R"?
         unique_types = ["R"] + unique_types
         # Rigid particles get type ID 0, move all others up by 1
-        typeids = np.concatenate(([0] * n_rigid), typeids + 1)
+        typeids = np.concatenate(
+                (np.array([0] * n_rigid), typeids + 1)
+        )
         # Update mass list and position list of Frame
         for idx, _id in enumerate(rigid_ids_set):
             group_indices = np.where(rigid_ids == _id)[0]
@@ -323,9 +325,9 @@ def _parse_particle_information(
             rigid_masses[idx] = sum(group_masses)
             rigid_xyz[idx] = com_xyz
         # Append rigid center mass and xyz to front
-        masses = np.concatenate(rigid_masses, masses)
-        xyz = np.concatenate(rigid_xyz, xyz)
-        rigid_id_tags = np.concatenate(np.arange(n_rigid), np.array(rigid_ids))
+        masses = np.concatenate((rigid_masses, masses))
+        xyz = np.concatenate((rigid_xyz, xyz))
+        rigid_id_tags = np.concatenate((np.arange(n_rigid), np.array(rigid_ids)))
 
     """
     Permittivity of free space = 2.39725e-4 e^2/((kcal/mol)(angstrom)),
@@ -349,7 +351,7 @@ def _parse_particle_information(
         if write_rigid:
             snapshot.particles.body[0:] = rigid_id_tags
     elif isinstance(snapshot, gsd.hoomd.Frame):
-        snapshot.particles.N = top.n_sites
+        snapshot.particles.N = top.n_sites + n_rigid
         snapshot.particles.types = unique_types
         snapshot.particles.position = xyz
         snapshot.particles.typeid = typeids

gmso/tests/test_hoomd.py

@@ -3,11 +3,9 @@
 import numpy as np
 import pytest
 import unyt as u
-from mbuild.formats.hoomd_forcefield import create_hoomd_forcefield
-
 from gmso import ForceField
 from gmso.external import from_mbuild
-from gmso.external.convert_hoomd import to_hoomd_forcefield, to_hoomd_snapshot
+from gmso.external.convert_hoomd import to_hoomd_forcefield, to_hoomd_snapshot, to_gsd_snapshot
 from gmso.parameterization import apply
 from gmso.tests.base_test import BaseTest
 from gmso.tests.utils import get_path
@@ -53,88 +51,31 @@ def run_hoomd_nvt(snapshot, forces, vhoomd=4):
     return sim
 
 
-@pytest.mark.skipif(not has_hoomd, reason="hoomd is not installed")
-@pytest.mark.skipif(not has_mbuild, reason="mbuild not installed")
-class TestGsd(BaseTest):
-    def test_mbuild_comparison(self, oplsaa_forcefield):
-        compound = mb.load("CCC", smiles=True)
-        com_box = mb.packing.fill_box(compound, box=[5, 5, 5], n_compounds=2)
-        base_units = {
-            "mass": u.g / u.mol,
-            "length": u.nm,
-            "energy": u.kJ / u.mol,
-        }
-
-        top = from_mbuild(com_box)
-        top.identify_connections()
-        top = apply(top, oplsaa_forcefield, remove_untyped=True)
-
-        gmso_snapshot, _ = to_hoomd_snapshot(top, base_units=base_units)
-        gmso_forces, _ = to_hoomd_forcefield(
-            top,
-            r_cut=1.4,
-            base_units=base_units,
-            pppm_kwargs={"resolution": (64, 64, 64), "order": 7},
-        )
-
-        integrator_forces = list()
-        for cat in gmso_forces:
-            for force in gmso_forces[cat]:
-                integrator_forces.append(force)
-
-        import foyer
-
-        oplsaa = foyer.Forcefield(name="oplsaa")
-        structure = oplsaa.apply(com_box)
 
-        d = 10
-        e = 1 / 4.184
-        m = 0.9999938574
 
-        mb_snapshot, mb_forcefield, _ = create_hoomd_forcefield(
-            structure,
-            ref_distance=d,
-            ref_energy=e,
-            ref_mass=m,
-            r_cut=1.4,
-            init_snap=None,
-            pppm_kwargs={"Nx": 64, "Ny": 64, "Nz": 64, "order": 7},
-        )
 
-        assert mb_snapshot.particles.N == gmso_snapshot.particles.N
-        assert np.allclose(
-            mb_snapshot.particles.position, gmso_snapshot.particles.position
-        )
-        assert mb_snapshot.bonds.N == gmso_snapshot.bonds.N
-        assert mb_snapshot.angles.N == gmso_snapshot.angles.N
-        assert mb_snapshot.dihedrals.N == gmso_snapshot.dihedrals.N
-
-        sorted_gmso_ff = sorted(integrator_forces, key=lambda cls: str(cls.__class__))
-        sorted_mbuild_ff = sorted(mb_forcefield, key=lambda cls: str(cls.__class__))
-
-        for mb_force, gmso_force in zip(sorted_mbuild_ff, sorted_gmso_ff):
-            if isinstance(
-                mb_force,
-                (
-                    hoomd.md.long_range.pppm.Coulomb,
-                    hoomd.md.pair.pair.LJ,
-                    hoomd.md.special_pair.LJ,
-                    hoomd.md.pair.pair.Ewald,
-                    hoomd.md.special_pair.Coulomb,
-                ),
-            ):
-                continue
-            keys = mb_force.params.param_dict.keys()
-            for key in keys:
-                gmso_key = key.replace("opls_135", "CT")
-                gmso_key = gmso_key.replace("opls_136", "CT")
-                gmso_key = gmso_key.replace("opls_140", "HC")
-                gmso_key = "-".join(sort_connection_strings(gmso_key.split("-")))
-                mb_params = mb_force.params.param_dict[key]
-                gmso_params = gmso_force.params.param_dict[gmso_key]
-                variables = mb_params.keys()
-                for var in variables:
-                    assert np.isclose(mb_params[var], gmso_params[var])
+@pytest.mark.skipif(not has_hoomd, reason="hoomd is not installed")
+@pytest.mark.skipif(not has_mbuild, reason="mbuild not installed")
+class TestGsd(BaseTest):
+    def test_rigid_bodies(self):
+        ethane = mb.lib.molecules.Ethane()
+        box = mb.fill_box(ethane, n_compounds=2, box=[2, 2, 2])
+        box_no_rigid = mb.clone(box)
+        for i, child in enumerate(box.children):
+            for p in child.particles():
+                p.rigid_id = i
+
+        top = from_mbuild(box)
+        top_no_rigid = from_mbuild(box_no_rigid)
+
+        rigid_ids = [site.rigid_id for site in top.sites]
+        assert len(rigid_ids) == box.n_particles
+        assert len(set(rigid_ids)) == 2
+
+        snapshot, refs = to_gsd_snapshot(top)
+        snapshot_no_rigid, refs = to_gsd_snapshot(top_no_rigid)
+        assert "R" in snapshot.particles.types
+        assert snapshot.particles.N - 2 == snapshot_no_rigid.particles.N
 
     @pytest.mark.skipif(
         int(hoomd_version[0]) < 4, reason="Unsupported features in HOOMD 3"