Test compiled Lennard Jones potential.

.github/workflows/requirements-test.txt

@@ -2,5 +2,5 @@ h5py==3.10.0
 gsd==3.2.1
 numpy==1.26.4
 PyYAML==6.0.1
-signac==2.1.0
+signac==2.2.0
 signac-flow==0.27.0

README.md

@@ -8,7 +8,7 @@ validation test workflows in this repository are organized into signac projects.
 * gsd >= 2.8.0
 * numpy
 * PyYAML
-* signac >= 2.0.0
+* signac >= 2.2.0
 * signac-flow >= 0.25.1
 * signac-dashboard [optional]
 * Simulation workflow steps require either the [glotzerlab-software container]

dashboard.py

@@ -20,44 +20,53 @@ class ValidationDashboard(Dashboard):
 
     def job_title(self, job):
         """Name jobs."""
-        if job.statepoint.subproject == 'lj_fluid':
+        if job.cached_statepoint['subproject'] == 'lj_fluid':
             return (
-                f'lj_fluid: kT={job.statepoint.kT}, '
-                f'rho={job.statepoint.density}, '
-                f'N={job.statepoint.num_particles}'
+                f'lj_fluid: kT={job.cached_statepoint["kT"]}, '
+                f'rho={job.cached_statepoint["density"]}, '
+                f'N={job.cached_statepoint["num_particles"]}'
             )
 
-        if job.statepoint.subproject == 'lj_union':
-            return f'lj_union: kT={job.statepoint.kT}, rho={job.statepoint.density}'
+        if job.cached_statepoint['subproject'] == 'lj_union':
+            return (
+                f'lj_union: kT={job.cached_statepoint["kT"]}, '
+                f'rho={job.cached_statepoint["density"]}'
+            )
 
-        if job.statepoint.subproject == 'alj_2d':
-            return f'alj_2d: kT={job.statepoint.kT}, rho={job.statepoint.density}'
+        if job.cached_statepoint['subproject'] == 'alj_2d':
+            return (
+                f'alj_2d: kT={job.cached_statepoint["kT"]}, '
+                f'rho={job.cached_statepoint["density"]}'
+            )
 
-        if job.statepoint.subproject in (
+        if job.cached_statepoint['subproject'] in (
             'hard_disk',
             'hard_sphere',
             'simple_polygon',
             'patchy_particle_pressure',
         ):
-            return f'{job.statepoint.subproject}: rho={job.statepoint.density}'
+            return (
+                f'{job.cached_statepoint["subproject"]}: '
+                f'rho={job.cached_statepoint["density"]}'
+            )
 
         raise RuntimeError('Unexpected job')
 
     def job_sorter(self, job):
         """Sort jobs."""
-        if job.statepoint.subproject == 'patchy_particle_pressure':
+        if job.cached_statepoint['subproject'] == 'patchy_particle_pressure':
             return (
-                job.statepoint.subproject,
-                job.statepoint.density,
-                job.statepoint.pressure,
-                job.statepoint.temperature,
-                job.statepoint.chi,
-                job.statepoint.replicate_idx,
+                job.cached_statepoint['subproject'],
+                job.cached_statepoint['density'],
+                job.cached_statepoint['pressure'],
+                job.cached_statepoint['temperature'],
+                job.cached_statepoint['chi'],
+                job.cached_statepoint['replicate_idx'],
             )
 
         return (
-            job.statepoint.subproject,
-            job.statepoint.num_particles,
+            job.cached_statepoint['subproject'],
+            job.cached_statepoint['num_particles'],
         )
 
 

hoomd_validation/alj_2d.py

@@ -59,7 +59,7 @@ def job_statepoints():
 
 def is_alj_2d(job):
     """Test if a given job is part of the alj_2d subproject."""
-    return job.statepoint['subproject'] == 'alj_2d'
+    return job.cached_statepoint['subproject'] == 'alj_2d'
 
 
 partition_jobs_cpu = aggregator.groupsof(
@@ -104,8 +104,8 @@ def alj_2d_create_initial_state(*jobs):
         message_filename=util.get_message_filename(job, 'create_initial_state.log'),
     )
 
-    num_particles = job.statepoint['num_particles']
-    density = job.statepoint['density']
+    num_particles = job.cached_statepoint['num_particles']
+    density = job.cached_statepoint['density']
 
     box_volume = num_particles / density
     L = box_volume ** (1 / 2.0)
@@ -231,7 +231,9 @@ def make_md_simulation(
     sim.operations.add(thermo)
 
     # thermalize momenta
-    sim.state.thermalize_particle_momenta(hoomd.filter.All(), job.sp.kT)
+    sim.state.thermalize_particle_momenta(
+        hoomd.filter.All(), job.cached_statepoint['kT']
+    )
 
     return sim
 
@@ -405,12 +407,12 @@ def alj_2d_conservation_analyze(*jobs):
             )
             job_energies[sim_mode] = (
                 job_energies[sim_mode] - job_energies[sim_mode][0]
-            ) / job.statepoint['num_particles']
+            ) / job.cached_statepoint['num_particles']
 
             momentum_vector = log_traj['hoomd-data/md/Integrator/linear_momentum']
             job_linear_momentum[sim_mode] = [
                 math.sqrt(v[0] ** 2 + v[1] ** 2 + v[2] ** 2)
-                / job.statepoint['num_particles']
+                / job.cached_statepoint['num_particles']
                 for v in momentum_vector
             ]
 
@@ -425,7 +427,7 @@ def plot(*, ax, data, quantity_name, legend=False):
                 ax.plot(
                     timesteps[i][mode],
                     data[i][mode],
-                    label=f'{mode}_{job.statepoint.replicate_idx}',
+                    label=f'{mode}_{job.cached_statepoint["replicate_idx"]}',
                 )
         ax.set_xlabel('time step')
         ax.set_ylabel(quantity_name)
@@ -442,13 +444,14 @@ def plot(*, ax, data, quantity_name, legend=False):
 
     fig.suptitle(
         'ALJ 2D conservation tests: '
-        f'$kT={job.statepoint.kT}$, $\\rho={job.statepoint.density}$, '
-        f'$N={job.statepoint.num_particles}$'
+        f'$kT={job.cached_statepoint["kT"]}$, '
+        f'$\\rho={job.cached_statepoint["density"]}$, '
+        f'$N={job.cached_statepoint["num_particles"]}$'
     )
     filename = (
-        f'alj_2d_conservation_kT{job.statepoint.kT}_'
-        f'density{round(job.statepoint.density, 2)}_'
-        f'N{job.statepoint.num_particles}.svg'
+        f'alj_2d_conservation_kT{job.cached_statepoint["kT"]}_'
+        f'density{round(job.cached_statepoint["density"], 2)}_'
+        f'N{job.cached_statepoint["num_particles"]}.svg'
     )
 
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')

hoomd_validation/hard_disk.py

@@ -49,7 +49,7 @@ def job_statepoints():
 
 def is_hard_disk(job):
     """Test if a given job is part of the hard_disk subproject."""
-    return job.statepoint['subproject'] == 'hard_disk'
+    return job.cached_statepoint['subproject'] == 'hard_disk'
 
 
 partition_jobs_cpu_serial = aggregator.groupsof(
@@ -93,8 +93,8 @@ def hard_disk_create_initial_state(*jobs):
     if communicator.rank == 0:
         print('starting hard_disk_create_initial_state:', job)
 
-    num_particles = job.statepoint['num_particles']
-    density = job.statepoint['density']
+    num_particles = job.cached_statepoint['num_particles']
+    density = job.cached_statepoint['density']
 
     box_volume = num_particles / density
     L = box_volume ** (1 / 2.0)
@@ -303,7 +303,7 @@ def run_npt_sim(job, device, complete_filename):
 
     # box updates
     boxmc = hoomd.hpmc.update.BoxMC(
-        betaP=job.statepoint.pressure, trigger=hoomd.trigger.Periodic(1)
+        betaP=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1)
     )
     boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6)
 
@@ -681,7 +681,7 @@ def hard_disk_analyze(job):
         timesteps=timesteps,
         data=densities,
         ylabel=r'$\rho$',
-        expected=job.sp.density,
+        expected=job.cached_statepoint['density'],
         max_points=500,
     )
     ax.legend()
@@ -692,14 +692,14 @@ def hard_disk_analyze(job):
         timesteps=timesteps,
         data=pressures,
         ylabel=r'$\beta P$',
-        expected=job.sp.pressure,
+        expected=job.cached_statepoint['pressure'],
         max_points=500,
     )
 
     fig.suptitle(
-        f'$\\rho={job.statepoint.density}$, '
-        f'$N={job.statepoint.num_particles}$, '
-        f'replicate={job.statepoint.replicate_idx}'
+        f'$\\rho={job.cached_statepoint["density"]}$, '
+        f'$N={job.cached_statepoint["num_particles"]}$, '
+        f'replicate={job.cached_statepoint["replicate_idx"]}'
     )
     fig.savefig(job.fn('nvt_npt_plots.svg'), bbox_inches='tight')
 

hoomd_validation/hard_sphere.py

@@ -44,7 +44,7 @@ def job_statepoints():
 
 def is_hard_sphere(job):
     """Test if a given job is part of the hard_sphere subproject."""
-    return job.statepoint['subproject'] == 'hard_sphere'
+    return job.cached_statepoint['subproject'] == 'hard_sphere'
 
 
 partition_jobs_cpu_serial = aggregator.groupsof(
@@ -88,8 +88,8 @@ def hard_sphere_create_initial_state(*jobs):
     if communicator.rank == 0:
         print('starting hard_sphere_create_initial_state:', job)
 
-    num_particles = job.statepoint['num_particles']
-    density = job.statepoint['density']
+    num_particles = job.cached_statepoint['num_particles']
+    density = job.cached_statepoint['density']
 
     box_volume = num_particles / density
     L = box_volume ** (1 / 3.0)
@@ -254,7 +254,7 @@ def run_npt_sim(job, device, complete_filename):
 
     # box updates
     boxmc = hoomd.hpmc.update.BoxMC(
-        betaP=job.statepoint.pressure, trigger=hoomd.trigger.Periodic(1)
+        betaP=job.cached_statepoint['pressure'], trigger=hoomd.trigger.Periodic(1)
     )
     boxmc.volume = dict(weight=1.0, mode='ln', delta=1e-6)
 
@@ -544,7 +544,7 @@ def hard_sphere_analyze(job):
         timesteps=timesteps,
         data=densities,
         ylabel=r'$\rho$',
-        expected=job.sp.density,
+        expected=job.cached_statepoint['density'],
         max_points=500,
     )
     ax.legend()
@@ -555,14 +555,14 @@ def hard_sphere_analyze(job):
         timesteps=timesteps,
         data=pressures,
         ylabel=r'$\beta P$',
-        expected=job.sp.pressure,
+        expected=job.cached_statepoint['pressure'],
         max_points=500,
     )
 
     fig.suptitle(
-        f'$\\rho={job.statepoint.density}$, '
-        f'$N={job.statepoint.num_particles}$, '
-        f'replicate={job.statepoint.replicate_idx}'
+        f'$\\rho={job.cached_statepoint["density"]}$, '
+        f'$N={job.cached_statepoint["num_particles"]}$, '
+        f'replicate={job.cached_statepoint["replicate_idx"]}'
     )
     fig.savefig(job.fn('nvt_npt_plots.svg'), bbox_inches='tight')