diff --git a/hoomd_validation/hard_disk.py b/hoomd_validation/hard_disk.py index e6178aa1..22fad6f3 100644 --- a/hoomd_validation/hard_disk.py +++ b/hoomd_validation/hard_disk.py @@ -327,7 +327,7 @@ def run_npt_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) + P=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) ) boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6) diff --git a/hoomd_validation/hard_sphere.py b/hoomd_validation/hard_sphere.py index 25bee4c9..4d8c623d 100644 --- a/hoomd_validation/hard_sphere.py +++ b/hoomd_validation/hard_sphere.py @@ -270,7 +270,7 @@ def run_npt_sim(job, device): initial_state = job.fn('initial_state.gsd') # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) + P=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) ) boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6) diff --git a/hoomd_validation/lj_fluid.py b/hoomd_validation/lj_fluid.py index da016c84..b39aba02 100644 --- a/hoomd_validation/lj_fluid.py +++ b/hoomd_validation/lj_fluid.py @@ -487,11 +487,11 @@ def make_mc_simulation(job, device, initial_state, sim_mode, extra_loggables=Non extra_loggables = [] # integrator - mc = hoomd.hpmc.integrate.Sphere(nselect=1) + mc = hoomd.hpmc.integrate.Sphere(nselect=1, kT=job.cached_statepoint['kT']) mc.shape['A'] = dict(diameter=0.0) # pair potential - epsilon = LJ_PARAMS['epsilon'] / job.cached_statepoint['kT'] # 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'] @@ -659,7 +659,7 @@ def run_npt_mc_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'] / job.cached_statepoint['kT'], + P=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1), ) boxmc.volume = dict(weight=1.0, mode='ln', delta=0.01) @@ -861,10 +861,9 @@ def analyze(*jobs): 'hoomd-data/md/compute/ThermodynamicQuantities/potential_energy' ] else: - energies[sim_mode] = ( - log_traj['hoomd-data/hpmc/pair/LennardJones/energy'] - * job.cached_statepoint['kT'] - ) + energies[sim_mode] = log_traj[ + 'hoomd-data/hpmc/pair/LennardJones/energy' + ] energies[sim_mode] /= job.cached_statepoint['num_particles'] @@ -1186,10 +1185,7 @@ def distribution_analyze(*jobs): ) else: potential_energy_samples[sim_mode].extend( - list( - log_traj['hoomd-data/hpmc/pair/LennardJones/energy'] - * job.cached_statepoint['kT'] - ) + 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 f635ac67..d1f176ae 100644 --- a/hoomd_validation/lj_union.py +++ b/hoomd_validation/lj_union.py @@ -517,14 +517,14 @@ def make_mc_simulation(job, device, initial_state, sim_mode, extra_loggables=Non extra_loggables = [] # integrator - mc = hoomd.hpmc.integrate.Sphere(nselect=1) + mc = hoomd.hpmc.integrate.Sphere(nselect=1, kT=job.cached_statepoint['kT']) mc.shape['A'] = dict(diameter=0.0) mc.shape['R'] = dict(diameter=0.0, orientable=True) # pair potential lennard_jones = hoomd.hpmc.pair.LennardJones() lennard_jones.params[('A', 'A')] = dict( - epsilon=LJ_PARAMS['epsilon'] / job.cached_statepoint['kT'], + epsilon=LJ_PARAMS['epsilon'], sigma=LJ_PARAMS['sigma'], r_on=LJ_PARAMS['r_on'], r_cut=LJ_PARAMS['r_cut'], @@ -691,7 +691,7 @@ def run_npt_mc_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'] / job.cached_statepoint['kT'], + P=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1), ) boxmc.volume = dict(weight=1.0, mode='ln', delta=0.01) @@ -905,10 +905,7 @@ def analyze(*jobs): 'hoomd-data/md/compute/ThermodynamicQuantities/potential_energy' ] else: - energies[sim_mode] = ( - log_traj['hoomd-data/hpmc/pair/Union/energy'] - * job.cached_statepoint['kT'] - ) + energies[sim_mode] = log_traj['hoomd-data/hpmc/pair/Union/energy'] energies[sim_mode] /= job.cached_statepoint['num_particles'] @@ -1236,7 +1233,6 @@ def distribution_analyze(*jobs): else: potential_energy_samples[sim_mode].extend( log_traj['hoomd-data/hpmc/pair/Union/energy'] - * job.cached_statepoint['kT'] ) if 'md' in sim_mode: diff --git a/hoomd_validation/patchy_particle_pressure.py b/hoomd_validation/patchy_particle_pressure.py index a1caff03..be126f40 100644 --- a/hoomd_validation/patchy_particle_pressure.py +++ b/hoomd_validation/patchy_particle_pressure.py @@ -103,7 +103,7 @@ def job_statepoints(): def make_potential( - delta_rad, sq_well_lambda, sigma, kT, long_range_interaction_scale_factor + delta_rad, sq_well_lambda, sigma, long_range_interaction_scale_factor ): """Make the Kern-Frenkel pair potential. @@ -129,8 +129,8 @@ def make_potential( sq_well_lambda * sigma, ] epsilon = [ - -1 / kT, - -1 / kT * long_range_interaction_scale_factor, + -1, + -1 * long_range_interaction_scale_factor, ] step = hoomd.hpmc.pair.Step() step.params[('A', 'A')] = dict(epsilon=epsilon, r=r) @@ -188,7 +188,7 @@ def create_initial_state(*jobs): # Use hard sphere + patches Monte Carlo to randomize the initial # configuration - mc = hoomd.hpmc.integrate.Sphere(default_d=0.05, default_a=0.1) + mc = hoomd.hpmc.integrate.Sphere(default_d=0.05, default_a=0.1, kT=temperature) diameter = 1.0 mc.shape['A'] = dict(diameter=diameter, orientable=True) delta = 2 * numpy.arcsin(numpy.sqrt(chi)) @@ -196,7 +196,6 @@ def create_initial_state(*jobs): delta, lambda_, diameter, - temperature, long_range_interaction_scale_factor, ) mc.pair_potentials = [angular_step] @@ -267,14 +266,13 @@ def make_mc_simulation(job, device, initial_state, sim_mode, extra_loggables=Non 'long_range_interaction_scale_factor' ] diameter = 1.0 - mc = hoomd.hpmc.integrate.Sphere(default_d=0.05, default_a=0.1) + mc = hoomd.hpmc.integrate.Sphere(default_d=0.05, default_a=0.1, kT=temperature) mc.shape['A'] = dict(diameter=diameter, orientable=True) delta = 2 * numpy.arcsin(numpy.sqrt(chi)) angular_step = make_potential( delta, lambda_, diameter, - temperature, long_range_interaction_scale_factor, ) mc.pair_potentials = [angular_step] @@ -285,7 +283,7 @@ def make_mc_simulation(job, device, initial_state, sim_mode, extra_loggables=Non logger = hoomd.logging.Logger(categories=['scalar', 'sequence']) logger.add(mc, quantities=['translate_moves']) - logger.add(sdf, quantities=['betaP']) + logger.add(sdf, quantities=['P']) logger.add(compute_density, quantities=['density']) logger.add(angular_step, quantities=['energy']) for loggable, quantity in extra_loggables: @@ -433,7 +431,8 @@ def run_npt_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'], 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) @@ -622,7 +621,7 @@ def analyze(*jobs): timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep'] - pressures[sim_mode] = log_traj['hoomd-data/hpmc/compute/SDF/betaP'] + pressures[sim_mode] = log_traj['hoomd-data/hpmc/compute/SDF/P'] densities[sim_mode] = log_traj[ 'hoomd-data/custom_actions/ComputeDensity/density' @@ -663,7 +662,7 @@ def analyze(*jobs): ax=ax, timesteps=timesteps, data=pressures, - ylabel=r'$\beta P$', + ylabel=r'$\P$', expected=job.cached_statepoint['pressure'], max_points=500, ) diff --git a/hoomd_validation/simple_polygon.py b/hoomd_validation/simple_polygon.py index 3648469c..fb65ea2b 100644 --- a/hoomd_validation/simple_polygon.py +++ b/hoomd_validation/simple_polygon.py @@ -350,7 +350,7 @@ def run_npt_sim(job, device): # box updates boxmc = hoomd.hpmc.update.BoxMC( - betaP=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) + P=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1) ) boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6)