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Update to freud 3.0, use get_molecule_cluster from cmeutils #79

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merged 2 commits into from
Jun 19, 2024
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Update to freud 3.0, use get_molecule_cluster from cmeutils #79

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5ee91d6
update env file, use snap mol cluster func from cmeutils instead of i…
chrisjonesBSU Jun 19, 2024
f40c005
use latest cmeutils version
chrisjonesBSU Jun 19, 2024
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11 changes: 5 additions & 6 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,18 @@ name: grits
channels:
- conda-forge
dependencies:
- cmeutils >= 1.2.0
- cmeutils >=1.3.0
- ele
- freud = 2.13.2
- gsd >= 3.0
- freud >=3.0
- gsd >=3.0
- jupyterlab
- mbuild
- mbuild >=0.17.1
- ele
- freud
- numpy
- openbabel
- pip
- pre-commit
- py3Dmol
- pytest
- pytest-cov
- python = 3.10
- python >=3.10
5 changes: 2 additions & 3 deletions grits/coarsegrain.py
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Expand Up @@ -10,7 +10,7 @@
import freud
import gsd.hoomd
import numpy as np
from cmeutils.gsd_utils import identify_snapshot_connections
from cmeutils.gsd_utils import get_molecule_cluster, identify_snapshot_connections
from ele import element_from_symbol
from mbuild import Compound, clone
from mbuild.utils.io import run_from_ipython
Expand All @@ -24,7 +24,6 @@
get_quaternion,
has_common_member,
has_number,
snap_molecules,
)

__all__ = ["CG_Compound", "CG_System", "Bead"]
Expand Down Expand Up @@ -574,7 +573,7 @@ def _get_compounds(
conversion_dict[i].symbol for i in snap.particles.types
]
# Break apart the snapshot into separate molecules
molecules = snap_molecules(snap)
molecules = get_molecule_cluster(snap=snap)
mol_inds = []
for i in range(max(molecules) + 1):
mol_inds.append(np.where(molecules == i)[0])
Expand Down
17 changes: 0 additions & 17 deletions grits/utils.py
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Expand Up @@ -82,23 +82,6 @@ def comp_from_snapshot(snapshot, indices, length_scale=1.0, mass_scale=1.0):
return comp


def snap_molecules(snap):
"""Get the molecule indices based on bonding in a gsd.hoomd.Frame."""
system = freud.AABBQuery.from_system(snap)
n_query_points = n_points = snap.particles.N
query_point_indices = snap.bonds.group[:, 0]
point_indices = snap.bonds.group[:, 1]
distances = system.box.compute_distances(
system.points[query_point_indices], system.points[point_indices]
)
nlist = freud.NeighborList.from_arrays(
n_query_points, n_points, query_point_indices, point_indices, distances
)
cluster = freud.cluster.Cluster()
cluster.compute(system=system, neighbors=nlist)
return cluster.cluster_idx


def align(compound, particle, towards_compound, around=None):
"""Spin a compound such that particle points at towards_compound.

Expand Down
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