Logger.add does not handle only_default as documented.

[joaander]

Description

Logger.add(instance, quantities=['some_non_default_quantity']) does not add the quantity as documented:

This is what the documentation states:

The only_default flag is mainly a convenience by allowing quantities not commonly logged (but available) to be passed over unless explicitly asked for. You can override the only_default flag by explicitly listing the quantities you want in add ...

Script

# Include a minimal script that reproduces the problem
import hoomd

cell = hoomd.md.nlist.Cell(buffer=0.4)
logger = hoomd.logging.Logger(categories=['scalar'])
logger.add(cell, quantities=['num_builds'])

print("logger items:")
for key,value in logger.items():
    print(key,value)

logger2 = hoomd.logging.Logger(categories=['scalar'], only_default=False)
logger2.add(cell, quantities=['num_builds'])

print("logger2 items:")
for key,value in logger2.items():
    print(key,value)

Output

logger items:
logger2 items:
('md', 'nlist', 'Cell', 'num_builds') <hoomd.logging._LoggerEntry object at 0x7fa45fbea740>
('md', 'nlist', 'Cell') {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea7a0>}
('md', 'nlist') {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea8f0>}}
('md',) {'nlist': {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbeace0>}}}

Expected output

logger items:
('md', 'nlist', 'Cell', 'num_builds') <hoomd.logging._LoggerEntry object at 0x7fa45fbea740>
('md', 'nlist', 'Cell') {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea7a0>}
('md', 'nlist') {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea8f0>}}
('md',) {'nlist': {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbeace0>}}}
logger2 items:
('md', 'nlist', 'Cell', 'num_builds') <hoomd.logging._LoggerEntry object at 0x7fa45fbea740>
('md', 'nlist', 'Cell') {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea7a0>}
('md', 'nlist') {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbea8f0>}}
('md',) {'nlist': {'Cell': {'num_builds': <hoomd.logging._LoggerEntry object at 0x7fa45fbeace0>}}}

Configuration

Platform:

• Mac
• Linux
• GPU
• CPU

Installation method:

• Compiled from source

Versions:

• Python version: 3.9
• HOOMD-blue version: trunk-minor

Developer

@b-butler can you look into this?

[joaander]

Fixed in #1331.