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Use HDF5 files for quantity logs. #72

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merged 9 commits into from
Nov 9, 2023
Merged

Use HDF5 files for quantity logs. #72

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b54cfad
Use HDF5 logger.
joaander Nov 6, 2023
2a89643
Fix h5 file creation.
joaander Nov 6, 2023
0265510
Add h5py to CI tests.
joaander Nov 6, 2023
b49195d
Read h5 log files.
joaander Nov 6, 2023
54036ea
Run pre-commit.
joaander Nov 6, 2023
b9012a0
Fix HDF5 log readers.
joaander Nov 6, 2023
4f05670
Fix performance issue when run with ENABLE_TBB=on build.
joaander Nov 7, 2023
bf4150f
Run pre-commit.
joaander Nov 7, 2023
257f435
Remove invalid comments.
joaander Nov 9, 2023
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7 changes: 4 additions & 3 deletions .github/workflows/requirements-test.txt
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Original file line number Diff line number Diff line change
@@ -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
15 changes: 8 additions & 7 deletions hoomd_validation/alj_2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 = []
Expand All @@ -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
Expand Down
42 changes: 20 additions & 22 deletions hoomd_validation/hard_disk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,20 +165,20 @@ def make_mc_simulation(job,
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'])
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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'],
Expand Down Expand Up @@ -399,21 +399,20 @@ def run_nec_sim(job, device, complete_filename):
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'],
Expand Down Expand Up @@ -588,7 +587,6 @@ 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
Expand All @@ -603,7 +601,7 @@ 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)
Expand All @@ -613,18 +611,18 @@ 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:
Expand Down Expand Up @@ -683,7 +681,7 @@ 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)
Expand Down
42 changes: 20 additions & 22 deletions hoomd_validation/hard_sphere.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,20 +160,20 @@ def make_mc_simulation(job,
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'])
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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'],
Expand Down Expand Up @@ -311,21 +311,20 @@ def run_nec_sim(job, device, complete_filename):
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'])
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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'],
Expand Down Expand Up @@ -467,7 +466,6 @@ 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
Expand All @@ -482,7 +480,7 @@ 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)
Expand All @@ -492,17 +490,17 @@ 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:
Expand Down Expand Up @@ -561,7 +559,7 @@ 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)
Expand Down
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