Merge pull request #72 from glotzerlab/log-hdf5

Use HDF5 files for quantity logs.
glotzerlab · Nov 9, 2023 · af73bc6 · af73bc6
2 parents e6ce7b1 + 257f435
commit af73bc6
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Showing 10 changed files with 191 additions and 186 deletions.
diff --git a/.github/workflows/requirements-test.txt b/.github/workflows/requirements-test.txt
@@ -1,5 +1,6 @@
-signac==2.1.0
-signac-flow==0.26.1
+h5py==3.10.0
+gsd==3.2.0
 numpy==1.26.1
 PyYAML==6.0.1
-gsd==3.2.0
+signac==2.1.0
+signac-flow==0.26.1
diff --git a/hoomd_validation/alj_2d.py b/hoomd_validation/alj_2d.py
@@ -349,7 +349,6 @@ def alj_2d_nve_md_job(*jobs):
                    aggregator=analysis_aggregator)
 def alj_2d_conservation_analyze(*jobs):
     """Analyze the output of NVE simulations and inspect conservation."""
-    import gsd.hoomd
     import math
     import matplotlib
     import matplotlib.style
@@ -359,7 +358,7 @@ def alj_2d_conservation_analyze(*jobs):
     print('starting alj_2d_conservation_analyze:', jobs[0])
 
     sim_modes = ['nve_md_cpu']
-    if os.path.exists(jobs[0].fn('nve_md_gpu_quantities.gsd')):
+    if os.path.exists(jobs[0].fn('nve_md_gpu_quantities.h5')):
         sim_modes.extend(['nve_md_gpu'])
 
     timesteps = []
@@ -372,20 +371,22 @@ def alj_2d_conservation_analyze(*jobs):
         job_linear_momentum = {}
 
         for sim_mode in sim_modes:
-            log_traj = gsd.hoomd.read_log(job.fn(sim_mode + '_quantities.gsd'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
-            job_timesteps[sim_mode] = log_traj['configuration/step']
+            job_timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 
             job_energies[sim_mode] = (
                 log_traj[
-                    'log/md/compute/ThermodynamicQuantities/potential_energy']
+                    'hoomd-data/md/compute/ThermodynamicQuantities/potential_energy']
                 + log_traj[
-                    'log/md/compute/ThermodynamicQuantities/kinetic_energy'])
+                    'hoomd-data/md/compute/ThermodynamicQuantities/kinetic_energy']
+            )
             job_energies[sim_mode] = (
                 job_energies[sim_mode]
                 - job_energies[sim_mode][0]) / job.statepoint["num_particles"]
 
-            momentum_vector = log_traj['log/md/Integrator/linear_momentum']
+            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"] for v in momentum_vector

diff --git a/hoomd_validation/hard_disk.py b/hoomd_validation/hard_disk.py
@@ -164,21 +164,20 @@ def make_mc_simulation(job,
     compute_density = ComputeDensity()
     sdf = hoomd.hpmc.compute.SDF(xmax=0.02, dx=1e-4)
 
-    # log to gsd
-    logger_gsd = hoomd.logging.Logger(categories=['scalar', 'sequence'])
-    logger_gsd.add(mc, quantities=['translate_moves'])
-    logger_gsd.add(sdf, quantities=['betaP'])
-    logger_gsd.add(compute_density, quantities=['density'])
+    logger = hoomd.logging.Logger(categories=['scalar', 'sequence'])
+    logger.add(mc, quantities=['translate_moves'])
+    logger.add(sdf, quantities=['betaP'])
+    logger.add(compute_density, quantities=['density'])
     for loggable, quantity in extra_loggables:
-        logger_gsd.add(loggable, quantities=[quantity])
+        logger.add(loggable, quantities=[quantity])
 
     # make simulation
     sim = util.make_simulation(job=job,
                                device=device,
                                initial_state=initial_state,
                                integrator=mc,
                                sim_mode=sim_mode,
-                               logger=logger_gsd,
+                               logger=logger,
                                table_write_period=WRITE_PERIOD,
                                trajectory_write_period=LOG_PERIOD['trajectory'],
                                log_write_period=LOG_PERIOD['quantities'],
@@ -398,22 +397,20 @@ def run_nec_sim(job, device, complete_filename):
     # compute the density
     compute_density = ComputeDensity()
 
-    # log to gsd
-    logger_gsd = hoomd.logging.Logger(categories=['scalar', 'sequence'])
-    logger_gsd.add(mc,
-                   quantities=[
-                       'translate_moves', 'particles_per_chain',
-                       'virial_pressure'
-                   ])
-    logger_gsd.add(compute_density, quantities=['density'])
+    logger = hoomd.logging.Logger(categories=['scalar', 'sequence'])
+    logger.add(mc,
+               quantities=[
+                   'translate_moves', 'particles_per_chain', 'virial_pressure'
+               ])
+    logger.add(compute_density, quantities=['density'])
 
     # make simulation
     sim = util.make_simulation(job=job,
                                device=device,
                                initial_state=initial_state,
                                integrator=mc,
                                sim_mode=sim_mode,
-                               logger=logger_gsd,
+                               logger=logger,
                                table_write_period=WRITE_PERIOD,
                                trajectory_write_period=LOG_PERIOD['trajectory'],
                                log_write_period=LOG_PERIOD['quantities'],
@@ -588,7 +585,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def hard_disk_analyze(job):
     """Analyze the output of all simulation modes."""
-    import gsd.hoomd
     import numpy
     import matplotlib
     import matplotlib.style
@@ -603,7 +599,7 @@ def hard_disk_analyze(job):
         'npt_cpu',
     ]
 
-    if os.path.exists(job.fn('nvt_gpu_quantities.gsd')):
+    if os.path.exists(job.fn('nvt_gpu_quantities.h5')):
         sim_modes.extend(['nvt_gpu'])
 
     util._sort_sim_modes(sim_modes)
@@ -613,18 +609,18 @@ def hard_disk_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = gsd.hoomd.read_log(job.fn(sim_mode + '_quantities.gsd'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
-        timesteps[sim_mode] = log_traj['configuration/step']
+        timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 
         if 'nec' in sim_mode:
             pressures[sim_mode] = log_traj[
-                'log/hpmc/nec/integrate/Sphere/virial_pressure']
+                'hoomd-data/hpmc/nec/integrate/Sphere/virial_pressure']
         else:
-            pressures[sim_mode] = log_traj['log/hpmc/compute/SDF/betaP']
+            pressures[sim_mode] = log_traj['hoomd-data/hpmc/compute/SDF/betaP']
 
         densities[sim_mode] = log_traj[
-            'log/custom_actions/ComputeDensity/density']
+            'hoomd-data/custom_actions/ComputeDensity/density']
 
     # save averages
     for mode in sim_modes:
@@ -683,7 +679,7 @@ def hard_disk_compare_modes(*jobs):
         'npt_cpu',
     ]
 
-    if os.path.exists(jobs[0].fn('nvt_gpu_quantities.gsd')):
+    if os.path.exists(jobs[0].fn('nvt_gpu_quantities.h5')):
         sim_modes.extend(['nvt_gpu'])
 
     util._sort_sim_modes(sim_modes)

diff --git a/hoomd_validation/hard_sphere.py b/hoomd_validation/hard_sphere.py
@@ -159,21 +159,20 @@ def make_mc_simulation(job,
     compute_density = ComputeDensity()
     sdf = hoomd.hpmc.compute.SDF(xmax=0.02, dx=1e-4)
 
-    # log to gsd
-    logger_gsd = hoomd.logging.Logger(categories=['scalar', 'sequence'])
-    logger_gsd.add(mc, quantities=['translate_moves'])
-    logger_gsd.add(sdf, quantities=['betaP'])
-    logger_gsd.add(compute_density, quantities=['density'])
+    logger = hoomd.logging.Logger(categories=['scalar', 'sequence'])
+    logger.add(mc, quantities=['translate_moves'])
+    logger.add(sdf, quantities=['betaP'])
+    logger.add(compute_density, quantities=['density'])
     for loggable, quantity in extra_loggables:
-        logger_gsd.add(loggable, quantities=[quantity])
+        logger.add(loggable, quantities=[quantity])
 
     # make simulation
     sim = util.make_simulation(job=job,
                                device=device,
                                initial_state=initial_state,
                                integrator=mc,
                                sim_mode=sim_mode,
-                               logger=logger_gsd,
+                               logger=logger,
                                table_write_period=WRITE_PERIOD,
                                trajectory_write_period=LOG_PERIOD['trajectory'],
                                log_write_period=LOG_PERIOD['quantities'],
@@ -310,22 +309,20 @@ def run_nec_sim(job, device, complete_filename):
     # compute the density
     compute_density = ComputeDensity()
 
-    # log to gsd
-    logger_gsd = hoomd.logging.Logger(categories=['scalar', 'sequence'])
-    logger_gsd.add(mc,
-                   quantities=[
-                       'translate_moves', 'particles_per_chain',
-                       'virial_pressure'
-                   ])
-    logger_gsd.add(compute_density, quantities=['density'])
+    logger = hoomd.logging.Logger(categories=['scalar', 'sequence'])
+    logger.add(mc,
+               quantities=[
+                   'translate_moves', 'particles_per_chain', 'virial_pressure'
+               ])
+    logger.add(compute_density, quantities=['density'])
 
     # make simulation
     sim = util.make_simulation(job=job,
                                device=device,
                                initial_state=initial_state,
                                integrator=mc,
                                sim_mode=sim_mode,
-                               logger=logger_gsd,
+                               logger=logger,
                                table_write_period=WRITE_PERIOD,
                                trajectory_write_period=LOG_PERIOD['trajectory'],
                                log_write_period=LOG_PERIOD['quantities'],
@@ -467,7 +464,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def hard_sphere_analyze(job):
     """Analyze the output of all simulation modes."""
-    import gsd.hoomd
     import numpy
     import matplotlib
     import matplotlib.style
@@ -482,7 +478,7 @@ def hard_sphere_analyze(job):
         'npt_cpu',
     ]
 
-    if os.path.exists(job.fn('nvt_gpu_quantities.gsd')):
+    if os.path.exists(job.fn('nvt_gpu_quantities.h5')):
         sim_modes.extend(['nvt_gpu'])
 
     util._sort_sim_modes(sim_modes)
@@ -492,17 +488,17 @@ def hard_sphere_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = gsd.hoomd.read_log(job.fn(sim_mode + '_quantities.gsd'))
-        timesteps[sim_mode] = log_traj['configuration/step']
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
+        timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 
         if 'nec' in sim_mode:
             pressures[sim_mode] = log_traj[
-                'log/hpmc/nec/integrate/Sphere/virial_pressure']
+                'hoomd-data/hpmc/nec/integrate/Sphere/virial_pressure']
         else:
-            pressures[sim_mode] = log_traj['log/hpmc/compute/SDF/betaP']
+            pressures[sim_mode] = log_traj['hoomd-data/hpmc/compute/SDF/betaP']
 
         densities[sim_mode] = log_traj[
-            'log/custom_actions/ComputeDensity/density']
+            'hoomd-data/custom_actions/ComputeDensity/density']
 
     # save averages
     for mode in sim_modes:
@@ -561,7 +557,7 @@ def hard_sphere_compare_modes(*jobs):
         'npt_cpu',
     ]
 
-    if os.path.exists(jobs[0].fn('nvt_gpu_quantities.gsd')):
+    if os.path.exists(jobs[0].fn('nvt_gpu_quantities.h5')):
         sim_modes.extend(['nvt_gpu'])
 
     util._sort_sim_modes(sim_modes)