diff --git a/hoomd_validation/lj_fluid.py b/hoomd_validation/lj_fluid.py index d48d7726..9d574aae 100644 --- a/hoomd_validation/lj_fluid.py +++ b/hoomd_validation/lj_fluid.py @@ -491,7 +491,7 @@ def make_mc_simulation(job, device, initial_state, sim_mode, extra_loggables=Non mc.shape['A'] = dict(diameter=0.0) # pair potential - epsilon = LJ_PARAMS['epsilon'] # noqa F841 + epsilon = LJ_PARAMS['epsilon'] # noqa F841 sigma = LJ_PARAMS['sigma'] r_on = job.cached_statepoint['r_on'] r_cut = job.cached_statepoint['r_cut'] @@ -861,9 +861,9 @@ def analyze(*jobs): 'hoomd-data/md/compute/ThermodynamicQuantities/potential_energy' ] else: - energies[sim_mode] = ( - log_traj['hoomd-data/hpmc/pair/LennardJones/energy'] - ) + energies[sim_mode] = log_traj[ + 'hoomd-data/hpmc/pair/LennardJones/energy' + ] energies[sim_mode] /= job.cached_statepoint['num_particles'] @@ -1185,9 +1185,7 @@ def distribution_analyze(*jobs): ) else: potential_energy_samples[sim_mode].extend( - list( - log_traj['hoomd-data/hpmc/pair/LennardJones/energy'] - ) + list(log_traj['hoomd-data/hpmc/pair/LennardJones/energy']) ) if 'md' in sim_mode: diff --git a/hoomd_validation/lj_union.py b/hoomd_validation/lj_union.py index 4f9bd7b3..d7430ef1 100644 --- a/hoomd_validation/lj_union.py +++ b/hoomd_validation/lj_union.py @@ -905,9 +905,7 @@ def analyze(*jobs): 'hoomd-data/md/compute/ThermodynamicQuantities/potential_energy' ] else: - energies[sim_mode] = ( - log_traj['hoomd-data/hpmc/pair/Union/energy'] - ) + energies[sim_mode] = log_traj['hoomd-data/hpmc/pair/Union/energy'] energies[sim_mode] /= job.cached_statepoint['num_particles'] diff --git a/hoomd_validation/patchy_particle_pressure.py b/hoomd_validation/patchy_particle_pressure.py index 429f8fd8..cce0049d 100644 --- a/hoomd_validation/patchy_particle_pressure.py +++ b/hoomd_validation/patchy_particle_pressure.py @@ -431,7 +431,8 @@ def run_npt_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - P=job.cached_statepoint['pressure']*job.cached_statepoint["temperature"], trigger=hoomd.trigger.Periodic(1) + P=job.cached_statepoint['pressure'] * job.cached_statepoint['temperature'], + trigger=hoomd.trigger.Periodic(1), ) boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6)