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glotzerlab · Oct 24, 2023 · 4e13f89 · 4e13f89
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Showing 8 changed files with 56 additions and 56 deletions.
diff --git a/hoomd_validation/alj_2d.py b/hoomd_validation/alj_2d.py
@@ -89,9 +89,9 @@ def alj_2d_create_initial_state(*jobs):
 
     init_diameter = CIRCUMCIRCLE_RADIUS * 2 * 1.15
 
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
 
     num_particles = job.statepoint['num_particles']
     density = job.statepoint['density']
@@ -320,9 +320,9 @@ def alj_2d_nve_md_job(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{sim_mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{sim_mode}_{device_name}.log'))
         run_nve_md_sim(job,
                        device,
                        complete_filename=f'{sim_mode}_{device_name}_complete')

diff --git a/hoomd_validation/hard_disk.py b/hoomd_validation/hard_disk.py
@@ -99,9 +99,9 @@ def hard_disk_create_initial_state(*jobs):
     position_2d = list(itertools.product(x, repeat=2))[:num_particles]
 
     # create snapshot
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
     snap = hoomd.Snapshot(communicator)
 
     if communicator.rank == 0:
@@ -564,9 +564,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{mode}_{device_name}.log'))
 
         globals().get(f'run_{mode}_sim')(
             job, device, complete_filename=f'{mode}_{device_name}_complete')

diff --git a/hoomd_validation/hard_sphere.py b/hoomd_validation/hard_sphere.py
@@ -94,9 +94,9 @@ def hard_sphere_create_initial_state(*jobs):
     position = list(itertools.product(x, repeat=3))[:num_particles]
 
     # create snapshot
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
     snap = hoomd.Snapshot(device.communicator)
 
     if device.communicator.rank == 0:
@@ -443,9 +443,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'run_{mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'run_{mode}_{device_name}.log'))
 
         globals().get(f'run_{mode}_sim')(
             job, device, complete_filename=f'{mode}_{device_name}_complete')

diff --git a/hoomd_validation/lj_fluid.py b/hoomd_validation/lj_fluid.py
@@ -109,9 +109,9 @@ def lj_fluid_create_initial_state(*jobs):
         print('starting lj_fluid_create_initial_state:', job)
 
     sp = job.sp
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
 
     box_volume = sp["num_particles"] / sp["density"]
     L = box_volume**(1 / 3.)
@@ -407,9 +407,9 @@ def md_sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{sim_mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{sim_mode}_{device_name}.log'))
 
         run_md_sim(job,
                    device,
@@ -806,9 +806,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{mode}_mc_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{mode}_mc_{device_name}.log'))
 
         globals().get(f'run_{mode}_mc_sim')(
             job, device, complete_filename=f'{mode}_mc_{device_name}_complete')
@@ -1339,9 +1339,9 @@ def lj_fluid_nve_md_job(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{sim_mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{sim_mode}_{device_name}.log'))
         run_nve_md_sim(job,
                        device,
                        run_length=run_length,

diff --git a/hoomd_validation/lj_union.py b/hoomd_validation/lj_union.py
@@ -97,9 +97,9 @@ def lj_union_create_initial_state(*jobs):
         print('starting lj_union_create_initial_state:', job)
 
     sp = job.sp
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
 
     box_volume = sp["num_particles"] / sp["density"]
     L = box_volume**(1 / 3.)
@@ -437,9 +437,9 @@ def md_sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{sim_mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{sim_mode}_{device_name}.log'))
 
         run_md_sim(job,
                    device,
@@ -864,9 +864,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{mode}_mc_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{mode}_mc_{device_name}.log'))
 
         globals().get(f'run_{mode}_mc_sim')(
             job, device, complete_filename=f'{mode}_mc_{device_name}_complete')
@@ -1419,9 +1419,9 @@ def lj_union_nve_md_job(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{sim_mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{sim_mode}_{device_name}.log'))
         run_nve_md_sim(job,
                        device,
                        run_length=run_length,

diff --git a/hoomd_validation/patchy_particle_pressure.py b/hoomd_validation/patchy_particle_pressure.py
@@ -190,9 +190,9 @@ def patchy_particle_pressure_create_initial_state(*jobs):
     position = list(itertools.product(x, repeat=3))[:num_particles]
 
     # create snapshot
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
     snap = hoomd.Snapshot(communicator)
 
     if communicator.rank == 0:
@@ -600,9 +600,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{mode}_{device_name}.log'))
 
         globals().get(f'run_{mode}_sim')(
             job, device, complete_filename=f'{mode}_{device_name}_complete')

diff --git a/hoomd_validation/simple_polygon.py b/hoomd_validation/simple_polygon.py
@@ -110,9 +110,9 @@ def simple_polygon_create_initial_state(*jobs):
     position_2d = list(itertools.product(x, repeat=2))[:num_particles]
 
     # create snapshot
-    device = hoomd.device.CPU(
-        communicator=communicator,
-        message_filename=util.get_message_filename(job, 'create_initial_state.log'))
+    device = hoomd.device.CPU(communicator=communicator,
+                              message_filename=util.get_message_filename(
+                                  job, 'create_initial_state.log'))
     snap = hoomd.Snapshot(communicator)
 
     if communicator.rank == 0:
@@ -486,9 +486,9 @@ def sampling_operation(*jobs):
         elif device_name == 'cpu':
             device_cls = hoomd.device.CPU
 
-        device = device_cls(
-            communicator=communicator,
-            message_filename=util.get_message_filename(job, f'{mode}_{device_name}.log'))
+        device = device_cls(communicator=communicator,
+                            message_filename=util.get_message_filename(
+                                job, f'{mode}_{device_name}.log'))
 
         globals().get(f'run_{mode}_sim')(
             job, device, complete_filename=f'{mode}_{device_name}_complete')

diff --git a/hoomd_validation/util.py b/hoomd_validation/util.py
@@ -30,14 +30,14 @@ def get_job_filename(sim_mode, device, name, type):
 
 
 def get_message_filename(job, filename):
-    """Get a cluster job unique message filename.
-    """
+    """Get a cluster job unique message filename."""
     cluster_id = os.environ.get('SLURM_JOB_ID', None)
     if cluster_id is not None:
         return job.fn(f'{cluster_id}-{filename}')
     else:
         return job.fn(filename)
 
+
 def run_up_to_walltime(sim, end_step, steps, walltime_stop):
     """Run a simulation, stopping early if a walltime limit is reached.