Fix HDF5 log readers.

glotzerlab · Nov 6, 2023 · b9012a0 · b9012a0
1 parent 54036ea
commit b9012a0
Show file tree

Hide file tree

Showing 8 changed files with 22 additions and 27 deletions.
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 h5py
     import math
     import matplotlib
     import matplotlib.style
@@ -372,8 +371,7 @@ def alj_2d_conservation_analyze(*jobs):
         job_linear_momentum = {}
 
         for sim_mode in sim_modes:
-            log_traj = h5py.File(mode='r',
-                                 name=job.fn(sim_mode + '_quantities.h5'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
             job_timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/hard_disk.py b/hoomd_validation/hard_disk.py
@@ -587,7 +587,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def hard_disk_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -612,7 +611,7 @@ def hard_disk_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
         timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/hard_sphere.py b/hoomd_validation/hard_sphere.py
@@ -466,7 +466,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def hard_sphere_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -491,7 +490,7 @@ def hard_sphere_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        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:

diff --git a/hoomd_validation/lj_fluid.py b/hoomd_validation/lj_fluid.py
@@ -831,7 +831,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def lj_fluid_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import math
     import matplotlib
@@ -871,7 +870,7 @@ def lj_fluid_analyze(job):
     linear_momentum = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
         timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 
@@ -1085,7 +1084,6 @@ def lj_fluid_compare_modes(*jobs):
                    aggregator=analysis_aggregator)
 def lj_fluid_distribution_analyze(*jobs):
     """Checks that MD follows the correct KE distribution."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -1144,8 +1142,7 @@ def lj_fluid_distribution_analyze(*jobs):
                 n_dof = num_particles * 3 - 3
 
             print('Reading' + job.fn(sim_mode + '_quantities.h5'))
-            log_traj = h5py.File(mode='r',
-                                 name=job.fn(sim_mode + '_quantities.h5'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
             if 'md' in sim_mode:
                 ke = log_traj[
@@ -1376,7 +1373,6 @@ def lj_fluid_nve_md_job(*jobs):
                    aggregator=nve_analysis_aggregator)
 def lj_fluid_conservation_analyze(*jobs):
     """Analyze the output of NVE simulations and inspect conservation."""
-    import h5py
     import numpy
     import math
     import matplotlib
@@ -1400,8 +1396,7 @@ def lj_fluid_conservation_analyze(*jobs):
         job_linear_momentum = {}
 
         for sim_mode in sim_modes:
-            log_traj = h5py.File(mode='r',
-                                 name=job.fn(sim_mode + '_quantities.h5'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
             job_timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/lj_union.py b/hoomd_validation/lj_union.py
@@ -890,7 +890,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def lj_union_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import math
     import matplotlib
@@ -930,7 +929,7 @@ def lj_union_analyze(job):
     linear_momentum = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
         timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 
@@ -1129,7 +1128,6 @@ def lj_union_compare_modes(*jobs):
                    aggregator=analysis_aggregator)
 def lj_union_distribution_analyze(*jobs):
     """Checks that MD follows the correct KE distribution."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -1196,8 +1194,7 @@ def lj_union_distribution_analyze(*jobs):
             n_rotate_dof = num_particles * 3
 
             print('Reading' + job.fn(sim_mode + '_quantities.h5'))
-            log_traj = h5py.File(mode='r',
-                                 name=job.fn(sim_mode + '_quantities.h5'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
             if 'md' in sim_mode:
                 # https://doi.org/10.1371/journal.pone.0202764
@@ -1453,7 +1450,6 @@ def lj_union_nve_md_job(*jobs):
                    aggregator=nve_analysis_aggregator)
 def lj_union_conservation_analyze(*jobs):
     """Analyze the output of NVE simulations and inspect conservation."""
-    import h5py
     import math
     import matplotlib
     import matplotlib.style
@@ -1476,8 +1472,7 @@ def lj_union_conservation_analyze(*jobs):
         job_linear_momentum = {}
 
         for sim_mode in sim_modes:
-            log_traj = h5py.File(mode='r',
-                                 name=job.fn(sim_mode + '_quantities.h5'))
+            log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
             job_timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/patchy_particle_pressure.py b/hoomd_validation/patchy_particle_pressure.py
@@ -594,7 +594,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def patchy_particle_pressure_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -615,7 +614,7 @@ def patchy_particle_pressure_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
         timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/simple_polygon.py b/hoomd_validation/simple_polygon.py
@@ -480,7 +480,6 @@ def sampling_operation(*jobs):
                                    executable=CONFIG["executable"]))
 def simple_polygon_analyze(job):
     """Analyze the output of all simulation modes."""
-    import h5py
     import numpy
     import matplotlib
     import matplotlib.style
@@ -501,7 +500,7 @@ def simple_polygon_analyze(job):
     densities = {}
 
     for sim_mode in sim_modes:
-        log_traj = h5py.File(mode='r', name=job.fn(sim_mode + '_quantities.h5'))
+        log_traj = util.read_log(job.fn(sim_mode + '_quantities.h5'))
 
         timesteps[sim_mode] = log_traj['hoomd-data/Simulation/timestep']
 

diff --git a/hoomd_validation/util.py b/hoomd_validation/util.py
@@ -6,6 +6,7 @@
 import numpy
 import signac
 import os
+import h5py
 
 
 def true_all(*jobs, key):
@@ -333,3 +334,13 @@ def plot_timeseries(ax,
 def _sort_sim_modes(sim_modes):
     """Sort simulation modes for comparison."""
     sim_modes.sort(key=lambda x: ('nvt' in x or 'nec' in x, 'md' in x, x))
+
+
+def read_log(filename):
+    """Read a HDF5 log as a dictionary of logged quantities."""
+    with h5py.File(mode='r', name=filename) as f:
+        keys = []
+        f.visit(lambda name: keys.append(name))
+        result = {key: numpy.array(f[key]) for key in keys}
+
+    return result