Enable flake8 for MPCD

.pre-commit-config.yaml

@@ -93,7 +93,6 @@ repos:
     exclude: |
       (?x)(
         ^hoomd/extern/|
-        ^hoomd/mpcd/|
         ^hoomd/metal/
       )
 - repo: https://github.com/pre-commit/mirrors-clang-format

hoomd/mpcd/__init__.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
-""" Multiparticle collision dynamics.
+"""Multiparticle collision dynamics.
 
 Simulating complex fluids and soft matter using conventional molecular dynamics
 methods (`hoomd.md`) can be computationally demanding due to large disparities

hoomd/mpcd/collide.py

@@ -97,11 +97,12 @@ class CollisionMethod(Operation):
 
     Args:
         period (int): Number of integration steps between collisions.
-        embedded_particles (hoomd.filter.filter_like): HOOMD particles to include in collision.
+        embedded_particles (hoomd.filter.filter_like): HOOMD particles to
+            include in collision.
 
     Attributes:
-        embedded_particles (hoomd.filter.filter_like): HOOMD particles to include
-            in collision (*read only*).
+        embedded_particles (hoomd.filter.filter_like): HOOMD particles to
+            include in collision (*read only*).
 
             These particles are included in per-cell quantities and have their
             velocities updated along with the MPCD particles.
@@ -118,10 +119,12 @@ class CollisionMethod(Operation):
                 will not be correctly transferred to the body. Support for this
                 is planned in future.
 
-        period (int): Number of integration steps between collisions (*read only*).
+        period (int): Number of integration steps between collisions
+            (*read only*).
 
-            A collision is executed each time the :attr:`~hoomd.Simulation.timestep`
-            is a multiple of `period`. It must be a multiple of `period` for the
+            A collision is executed each time the
+            :attr:`~hoomd.Simulation.timestep` is a multiple of `period`. It
+            must be a multiple of `period` for the
             :class:`~hoomd.mpcd.stream.StreamingMethod` if one is attached to
             the :class:`~hoomd.mpcd.Integrator`.
 
@@ -166,7 +169,9 @@ class AndersenThermostat(CollisionMethod):
 
     .. code-block:: python
 
-        andersen_thermostat = hoomd.mpcd.collide.AndersenThermostat(period=1, kT=1.0)
+        andersen_thermostat = hoomd.mpcd.collide.AndersenThermostat(
+            period=1,
+            kT=1.0)
         simulation.operations.integrator.collision_method = andersen_thermostat
 
     Collision including embedded particles.

hoomd/mpcd/fill.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
-r""" MPCD virtual-particle fillers.
+r"""MPCD virtual-particle fillers.
 
 Virtual particles are MPCD solvent particles that are added to ensure MPCD
 collision cells that are sliced by solid boundaries do not become "underfilled".
@@ -119,7 +119,8 @@ class GeometryFiller(VirtualParticleFiller):
         simulation.operations.integrator.virtual_particle_fillers = [filler]
 
     Attributes:
-        geometry (hoomd.mpcd.geometry.Geometry): Surface to fill around (*read only*).
+        geometry (hoomd.mpcd.geometry.Geometry): Surface to fill around
+            (*read only*).
 
     """
 
@@ -147,7 +148,8 @@ def _attach_hook(self):
         if isinstance(sim.device, hoomd.device.GPU):
             class_info[1] += "GPU"
         class_ = getattr(*class_info, None)
-        assert class_ is not None, "Virtual particle filler for geometry not found"
+        assert class_ is not None, ("Virtual particle filler for geometry"
+                                    " not found")
 
         self._cpp_obj = class_(
             sim.state._cpp_sys_def,

hoomd/mpcd/force.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
-r""" MPCD solvent forces.
+r"""MPCD solvent forces.
 
 MPCD can apply a body force to each MPCD particle as a function of position.
 The external force should be compatible with the chosen
@@ -46,10 +46,10 @@ class BlockForce(SolventForce):
             blocks.
         half_width (float): Half the width of each block.
 
-    The `force` magnitude *F* is applied in the *x* direction on the solvent particles
-    in blocks defined along the *y* direction by the `half_separation` *H* and
-    the `half_width` *w*. The force in *x* is :math:`+F` in the upper block,
-    :math:`-F` in the lower block, and zero otherwise.
+    The `force` magnitude *F* is applied in the *x* direction on the solvent
+    particles in blocks defined along the *y* direction by the `half_separation`
+    *H* and the `half_width` *w*. The force in *x* is :math:`+F` in the upper
+    block, :math:`-F` in the lower block, and zero otherwise.
 
     .. math::
         :nowrap:
@@ -62,9 +62,9 @@ class BlockForce(SolventForce):
         \end{cases}
         \end{equation}
 
-    The `BlockForce` can be used to implement the double-parabola method for measuring
-    viscosity by setting :math:`H = L_y/4` and :math:`w = L_y/4`, where :math:`L_y` is
-    the size of the simulation box in *y*.
+    The `BlockForce` can be used to implement the double-parabola method for
+    measuring viscosity by setting :math:`H = L_y/4` and :math:`w = L_y/4`,
+    where :math:`L_y` is the size of the simulation box in *y*.
 
     Warning:
         You should define the blocks to lie fully within the simulation box and
@@ -77,7 +77,10 @@ class BlockForce(SolventForce):
     .. code-block:: python
 
         Ly = simulation.state.box.Ly
-        force = hoomd.mpcd.force.BlockForce(force=1.0, half_separation=Ly/4, half_width=Ly/4)
+        force = hoomd.mpcd.force.BlockForce(
+            force=1.0,
+            half_separation=Ly/4,
+            half_width=Ly/4)
         stream = hoomd.mpcd.stream.Bulk(period=1, solvent_force=force)
         simulation.operations.integrator.streaming_method = stream
 
@@ -135,9 +138,9 @@ class ConstantForce(SolventForce):
 
     The same constant force is applied to all solvent particles, independently
     of time and position. This force is useful for simulating pressure-driven
-    flow in conjunction with a confined geometry having no-slip boundary conditions.
-    It is also useful for measuring diffusion coefficients with nonequilibrium
-    methods.
+    flow in conjunction with a confined geometry having no-slip boundary
+    conditions. It is also useful for measuring diffusion coefficients with
+    nonequilibrium methods.
 
     .. rubric:: Example:
 

hoomd/mpcd/geometry.py

@@ -6,8 +6,10 @@
 A geometry defines solid boundaries that cannot be penetrated. These
 geometries are used for various operations in the MPCD algorithm including:
 
-* Bounce-back streaming for MPCD particles (:class:`hoomd.mpcd.stream.BounceBack`)
-* Bounce-back integration for MD particles (:class:`hoomd.mpcd.methods.BounceBack`)
+* Bounce-back streaming for MPCD particles
+  (:class:`hoomd.mpcd.stream.BounceBack`)
+* Bounce-back integration for MD particles
+  (:class:`hoomd.mpcd.methods.BounceBack`)
 * Virtual particle filling (:class:`hoomd.mpcd.fill.GeometryFiller`)
 
 Each geometry may put constraints on the size of the simulation and where

hoomd/mpcd/integrate.py

@@ -1,6 +1,8 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+"""Implement MPCD Integrator."""
+
 import hoomd
 from hoomd.data.parameterdicts import ParameterDict
 from hoomd.data import syncedlist
@@ -48,7 +50,8 @@ class Integrator(_MDIntegrator):
         collision_method (hoomd.mpcd.collide.CollisionMethod): Collision method
             for the MPCD solvent and any embedded particles.
 
-        virtual_particle_fillers (Sequence[hoomd.mpcd.fill.VirtualParticleFiller]): Solvent
+        virtual_particle_fillers
+            (Sequence[hoomd.mpcd.fill.VirtualParticleFiller]): Solvent
             virtual-particle filler(s).
 
         solvent_sorter (hoomd.mpcd.tune.ParticleSorter): Tuner for sorting the
@@ -86,7 +89,9 @@ class Integrator(_MDIntegrator):
     .. code-block:: python
 
         stream = hoomd.mpcd.stream.Bulk(period=1)
-        collide = hoomd.mpcd.collide.StochasticRotationDynamics(period=1, angle=130)
+        collide = hoomd.mpcd.collide.StochasticRotationDynamics(
+            period=1,
+            angle=130)
         integrator = hoomd.mpcd.Integrator(
             dt=0.1,
             streaming_method=stream,
@@ -213,10 +218,8 @@ def cell_list(self):
 
     @property
     def virtual_particle_fillers(self):
-        """Sequence[hoomd.mpcd.fill.VirtualParticleFiller]: Solvent
-            virtual-particle fillers.
-
-        """
+        """Sequence[hoomd.mpcd.fill.VirtualParticleFiller]: Solvent \
+        virtual-particle fillers."""
         return self._virtual_particle_fillers
 
     @virtual_particle_fillers.setter
@@ -261,7 +264,7 @@ def _setattr_param(self, attr, value):
             if value is not None and value._attached:
                 raise ValueError("Cannot attach to multiple integrators.")
 
-            # if already attached, change out which is attached, then set parameter
+            # if already attached, change out and set parameter
             if self._attached:
                 if cur_value is not None:
                     cur_value._detach()

hoomd/mpcd/methods.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
-r""" MPCD integration methods
+r"""MPCD integration methods.
 
 Extra integration methods for solutes (MD particles) embedded in an MPCD
 solvent. These methods are not restricted to MPCD simulations: they can be used
@@ -31,54 +31,54 @@ class BounceBack(Method):
             apply this method.
         geometry (hoomd.mpcd.geometry.Geometry): Surface to bounce back from.
 
-    A bounce-back method for integrating solutes (MD particles) embedded in
-    an MPCD solvent. The integration scheme is velocity Verlet with bounce-back
+    A bounce-back method for integrating solutes (MD particles) embedded in an
+    MPCD solvent. The integration scheme is velocity Verlet with bounce-back
     performed at the solid boundaries defined by a geometry, as in
     `hoomd.mpcd.stream.BounceBack`. This gives a simple approximation of the
-    interactions required to keep a solute bounded in a geometry, and more complex
-    interactions can be specified, for example, by writing custom external fields.
-
-    Similar caveats apply to these methods as for `hoomd.mpcd.stream.BounceBack`.
-    In particular:
-
-    1. The simulation box is periodic, but the `geometry` may impose non-periodic
-       boundary conditions. You must ensure that the box is sufficiently large to
-       enclose the `geometry` and that all particles lie inside it, or an error will
-       be raised at runtime.
-    2. You must also ensure that particles do not self-interact through the periodic
-       boundaries. This is usually achieved for simple pair potentials by padding
-       the box size by the largest cutoff radius. Failure to do so may result in
-       unphysical interactions.
+    interactions required to keep a solute bounded in a geometry, and more
+    complex interactions can be specified, for example, by writing custom
+    external fields.
+
+    Similar caveats apply to these methods as for
+    `hoomd.mpcd.stream.BounceBack`. In particular:
+
+    1. The simulation box is periodic, but the `geometry` may impose
+       non-periodic boundary conditions. You must ensure that the box is
+       sufficiently large to enclose the `geometry` and that all particles lie
+       inside it, or an error will be raised at runtime.
+    2. You must also ensure that particles do not self-interact through the
+       periodic boundaries. This is usually achieved for simple pair potentials
+       by padding the box size by the largest cutoff radius. Failure to do so
+       may result in unphysical interactions.
     3. Bounce-back rules do not always enforce no-slip conditions at surfaces
-       properly. It may still be necessary to add additional "ghost" MD particles in
-       the surface to achieve the right boundary conditions and reduce density
-       fluctuations.
+       properly. It may still be necessary to add additional "ghost" MD
+       particles in the surface to achieve the right boundary conditions and
+       reduce density fluctuations.
 
     Warning:
 
-        This method does not support anisotropic integration because
-        torques are not computed for collisions with the boundary.
-        Rigid bodies will also not be treated correctly because the
-        integrator is not aware of the extent of the particles. The surface
-        reflections are treated as point particles. These conditions are too
-        complicated to validate easily, so it is the user's responsibility to
-        choose the `filter` correctly.
+        This method does not support anisotropic integration because torques are
+        not computed for collisions with the boundary. Rigid bodies will also
+        not be treated correctly because the integrator is not aware of the
+        extent of the particles. The surface reflections are treated as point
+        particles. These conditions are too complicated to validate easily, so
+        it is the user's responsibility to choose the `filter` correctly.
 
     .. rubric:: Example:
 
     .. code-block:: python
 
         plates = hoomd.mpcd.geometry.ParallelPlates(H=3.0)
         nve = hoomd.mpcd.methods.BounceBack(
-            filter=hoomd.filter.All(),
-            geometry=plates)
+            filter=hoomd.filter.All(), geometry=plates)
         simulation.operations.integrator.methods.append(nve)
 
     Attributes:
         filter (hoomd.filter.filter_like): Subset of particles on which to apply
             this method (*read only*).
 
-        geometry (hoomd.mpcd.geometry.Geometry): Surface to bounce back from (*read only*).
+        geometry (hoomd.mpcd.geometry.Geometry): Surface to bounce back from
+            (*read only*).
 
     """
 

hoomd/mpcd/pytest/test_collide.py

@@ -1,9 +1,10 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import pytest
+
 import hoomd
 from hoomd.conftest import pickling_check
-import pytest
 
 
 @pytest.fixture

hoomd/mpcd/pytest/test_fill.py

@@ -1,10 +1,10 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import pytest
+
 import hoomd
 from hoomd.conftest import pickling_check
-import numpy as np
-import pytest
 
 
 @pytest.fixture

hoomd/mpcd/pytest/test_force.py

@@ -1,10 +1,10 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import numpy as np
+
 import hoomd
 from hoomd.conftest import pickling_check
-import numpy as np
-import pytest
 
 
 def test_block_force(simulation_factory):

hoomd/mpcd/pytest/test_geometry.py

@@ -1,9 +1,10 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import pytest
+
 import hoomd
 from hoomd.conftest import pickling_check
-import pytest
 
 
 @pytest.fixture

hoomd/mpcd/pytest/test_integrator.py

@@ -1,12 +1,11 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import pytest
+
 import hoomd
 from hoomd.conftest import pickling_check
 
-import numpy as np
-import pytest
-
 
 @pytest.fixture
 def make_simulation(simulation_factory):

hoomd/mpcd/pytest/test_methods.py

@@ -1,11 +1,12 @@
 # Copyright (c) 2009-2023 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
-import hoomd
-from hoomd.conftest import pickling_check
 import numpy as np
 import pytest
 
+import hoomd
+from hoomd.conftest import pickling_check
+
 
 @pytest.fixture
 def snap():
@@ -103,7 +104,7 @@ def test_step_slip(self, simulation_factory, snap, integrator):
                 snap.particles.velocity,
                 [[1.0, -1.0, -1.0], [-1.0, -1.0, -1.0]])
 
-        # take another step, reflecting the perpendicular motion of second particle
+        # take another step, reflecting perpendicular motion of second particle
         sim.run(1)
         snap = sim.state.get_snapshot()
         if snap.communicator.rank == 0: