remove rigid body help funcs and tests, pin freud verisons

cmeutils/gsd_utils.py

@@ -7,8 +7,6 @@
 import numpy as np
 from boltons.setutils import IndexedSet
 
-from cmeutils.geometry import moit
-
 
 def frame_to_freud_system(frame, ref_length=None):
     """Creates a freud system given a gsd.hoomd.Frame.
@@ -217,107 +215,6 @@ def snap_delete_types(snap, delete_types):
     return new_snap
 
 
-def create_rigid_snapshot(mb_compound):
-    """Preps a hoomd snapshot to store rigid body information
-
-    This method relies on using built-in mBuild methods to
-    create the rigid body information.
-
-    Parameters
-    ----------
-    mb_compound : mbuild.Compound, required
-        mBuild compound containing the rigid body information
-        of the complete system
-
-    Returns
-    -------
-    hoomd.Snapshot
-        A snapshot that contains the needed place-holder particles
-        to set up a rigid body simulation in HoomdBlue Version 3.
-        Pass this snapshot into the `init_snap` parameter
-        of mBuild's `create_hoomd_forcefield` function.
-
-    """
-    import hoomd
-
-    rigid_ids = [p.rigid_id for p in mb_compound.particles()]
-    rigid_bodies = set(rigid_ids)
-    # Total number of rigid particles
-    N_mols = len(rigid_bodies)
-    init_snap = hoomd.Snapshot()
-    # Create place holder spots in the snapshot for rigid centers
-    init_snap.particles.types = ["R"]
-    init_snap.particles.N = N_mols
-    return init_snap
-
-
-def update_rigid_snapshot(snapshot, mb_compound):
-    """Update a snapshot prepared for rigid bodies with system informaiton
-
-    Parameters
-    ----------
-    snapshot : gsd.hoomd.Frame
-        The snapshot returned from create_hoomd_forcefield
-        or create_hoomd_simulation in mBuild
-    mb_compound : mbuild.Compound, required
-        mBuild compound containing the rigid body information
-        of the complete system
-
-    """
-    import hoomd
-
-    rigid_ids = [p.rigid_id for p in mb_compound.particles()]
-    rigid_bodies = set(rigid_ids)
-    # Total number of rigid body particles
-    N_mols = len(rigid_bodies)
-    N_p = [rigid_ids.count(i) for i in rigid_bodies]
-    # Right now, we're assuming each molecule has the same num of particles
-    assert len(set(N_p)) == 1
-    N_p = N_p[0]  # Number of particles per molecule
-    mol_inds = [
-        np.arange(N_mols + i * N_p, N_mols + i * N_p + N_p)
-        for i in range(N_mols)
-    ]
-
-    for i, inds in enumerate(mol_inds):
-        total_mass = np.sum(snapshot.particles.mass[inds])
-        com = (
-            np.sum(
-                snapshot.particles.position[inds]
-                * snapshot.particles.mass[inds, np.newaxis],
-                axis=0,
-            )
-            / total_mass
-        )
-        snapshot.particles.position[i] = com
-        snapshot.particles.body[i] = i
-        snapshot.particles.body[inds] = i * np.ones_like(inds)
-        snapshot.particles.mass[i] = np.sum(snapshot.particles.mass[inds])
-        snapshot.particles.moment_inertia[i] = moit(
-            snapshot.particles.position[inds],
-            snapshot.particles.mass[inds],
-            center=com,
-        )
-
-    rigid = hoomd.md.constrain.Rigid()
-    inds = mol_inds[0]
-    r_pos = snapshot.particles.position[0]
-    c_pos = snapshot.particles.position[inds]
-    c_pos -= r_pos
-    c_pos = [tuple(i) for i in c_pos]
-    c_types = [
-        snapshot.particles.types[i] for i in snapshot.particles.typeid[inds]
-    ]
-    c_orient = [tuple(i) for i in snapshot.particles.orientation[inds]]
-
-    rigid.body["R"] = {
-        "constituent_types": c_types,
-        "positions": c_pos,
-        "orientations": c_orient,
-    }
-    return snapshot, rigid
-
-
 def ellipsoid_gsd(gsd_file, new_file, ellipsoid_types, lpar, lperp):
     """Add needed information to GSD file to visualize ellipsoids.
 

cmeutils/tests/test_gsd.py

@@ -6,19 +6,16 @@
 import pytest
 from base_test import BaseTest
 from gmso.external import from_mbuild, to_gsd_snapshot
-from mbuild.formats.hoomd_forcefield import to_hoomdsnapshot
 
 from cmeutils.gsd_utils import (
     _validate_inputs,
-    create_rigid_snapshot,
     ellipsoid_gsd,
     frame_to_freud_system,
     get_all_types,
     get_molecule_cluster,
     get_type_position,
     identify_snapshot_connections,
     snap_delete_types,
-    update_rigid_snapshot,
     xml_to_gsd,
 )
 
@@ -47,28 +44,6 @@ def test_ellipsoid_gsd(self, butane_gsd):
             snap = f[-1]
         assert snap.particles.type_shapes[0]["type"] == "Ellipsoid"
 
-    def test_create_rigid_snapshot(self):
-        benzene = mb.load("c1ccccc1", smiles=True)
-        benzene.name = "Benzene"
-        box = mb.fill_box(benzene, 5, box=[3, 3, 3], seed=42)
-        box.label_rigid_bodies(discrete_bodies="Benzene")
-
-        rigid_init_snap = create_rigid_snapshot(box)
-        assert rigid_init_snap.particles.N == 5
-        assert rigid_init_snap.particles.types == ["R"]
-
-    def test_update_rigid_snapshot(self):
-        benzene = mb.load("c1ccccc1", smiles=True)
-        benzene.name = "Benzene"
-        box = mb.fill_box(benzene, 5, box=[3, 3, 3], seed=42)
-        box.label_rigid_bodies(discrete_bodies="Benzene")
-
-        rigid_init_snap = create_rigid_snapshot(box)
-        _snapshot, refs = to_hoomdsnapshot(box, hoomd_snapshot=rigid_init_snap)
-        snap, rigid_obj = update_rigid_snapshot(_snapshot, box)
-        assert snap.particles.N == 65
-        assert np.array_equal(snap.particles.typeid[0:5], np.array([0] * 5))
-
     def test_get_type_position(self, gsdfile):
         pos_array = get_type_position(gsd_file=gsdfile, typename="A")
         assert type(pos_array) is type(np.array([]))

environment-dev.yml

@@ -2,7 +2,7 @@ name: cmeutils-dev
 channels:
   - conda-forge
 dependencies:
-  - freud >= 3.0
+  - freud >= 3.0,<3.2
   - gmso >=0.11.2
   - fresnel >=0.13.5
   - gsd >=3.0

environment.yml

@@ -2,7 +2,7 @@ name: cmeutils
 channels:
   - conda-forge
 dependencies:
-  - freud >= 3.0
+  - freud >= 3.0,<3.2
   - gmso >=0.11.2
   - fresnel >=0.13.5
   - gsd >=3.0