Table logger logs small positive values incorrectly

[Charlottez112]

Description

Table logger logs positive values that are very close to 0 as 0.000... instead of with scientific notation.

Script

# I found this bug when I was logging harmonic bond energy for calculating free energies with the Einstein molecule method. When the spring is set to a very small value, the harmonic bond energy is logged as 0.
# Below is the code only associated with creating the table logger

logger = hoomd.logging.Logger(categories=['scalar'])
logger.add(sim, quantities=['timestep'])
logger.add(thermodynamic_properties, quantities=['kinetic_temperature', 'pressure', 'volume', 'potential_energy'])
logger.add(potential, quantities=['energy'])
logger.add(harmonic, quantities=['energy'])
data_file = open(f'data.log', mode='w', newline='\n')
data_logger = hoomd.write.Table(output=data_file,
                                trigger=hoomd.trigger.Periodic(period=100, phase=0),
                                logger=logger,
                                header_sep='_',
                                delimiter='\t')
sim.operations.writers.append(data_logger)

sim.run(500)

Input files

No response

Output

# md_bond_Harmonic_energy
0.00000

Expected output

With a gsd logger, this value is around 2.3568318406061576e-14

Platform

GPU

Installation method

glotzerlab-software container

HOOMD-blue version

3.10.0

Python version

3.9.5