hoomd.write.GSD not recognizing "dynamic" strings for loggable quantities

[jackdwwalker]

Hello all,

I'm working on a molecular dynamics project using HOOMD 3.11, and when trying to add additional dynamic quantities to my GSD writer (velocity, typeid, etc...), I'm finding that the writer is not recognizing the "member strings" as outlined in this doc.

If I include one of the "category" strings in the dynamic list, it works fine and correctly records all the members in that category (ie "momentum" is writing velocities properly), but trying to use individual strings (ex: "particles/velocity") gives the following output:

start build lattice build complete Using environment configuration: CACFrontenac start equilibrate starting job kT1 defined r_cut & equil time defined time step defined notice(2): Using domain decomposition: n_x = 4 n_y = 4 n_z = 4. state created from lattice neighborList with buffer, integrator, & lj potential created lj A-A interaction defined & added to integrator NPT operation added to integrator, integrator assigned to sim logger initialized with timestep and thermo properties Using environment configuration: CACFrontenac Traceback (most recent call last): File "/global/home/hpc5610/455_thesis/hoomd/2025_summer_proj/directory_template/operations.py", line 709, in <module> FlowProject().main() File "/global/home/hpc5610/.local/lib/python3.8/site-packages/flow/project.py", line 5125, in main args.func(args) File "/global/home/hpc5610/.local/lib/python3.8/site-packages/flow/project.py", line 4874, in _main_exec operation_function(*aggregate) File "/global/home/hpc5610/.local/lib/python3.8/site-packages/flow/project.py", line 625, in __call__ return self._op_func(*jobs) File "/global/home/hpc5610/455_thesis/hoomd/2025_summer_proj/directory_template/operations.py", line 168, in equilibrate sim.operations.writers.append(gsd_writer) File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.8.10/lib/python3.8/_collections_abc.py", line 962, in append self.insert(len(self), value) File "/global/home/hpc5610/455_thesis/hoomd/src/install/lib/python3.8/site-packages/hoomd/data/syncedlist.py", line 139, in insert self._register_item(value) File "/global/home/hpc5610/455_thesis/hoomd/src/install/lib/python3.8/site-packages/hoomd/data/syncedlist.py", line 188, in _register_item value._attach(self._simulation) File "/global/home/hpc5610/455_thesis/hoomd/src/install/lib/python3.8/site-packages/hoomd/operation.py", line 301, in _attach self._attach_hook() File "/global/home/hpc5610/455_thesis/hoomd/src/install/lib/python3.8/site-packages/hoomd/write/gsd.py", line 198, in _attach_hook raise RuntimeError( RuntimeError: GSD: dynamic quantity particles/typeid is not valid

This is just for one operation in a series of them (I'm using signac flow), but I have the exact same issue regardless of which operation it is, and other than problem everything runs exactly as expected. The full code for this operation is attached below:

`
@spike_prep
@full_run
@FlowProject.pre.isfile("lattice_snap.gsd")
@FlowProject.post.isfile("equilibrate_snap.gsd")
@FlowProject.operation(directives={"nranks":N_ranks, "np":N_ranks, "memory":mem_per_CPU*N_ranks, "walltime":walltime})
def equilibrate(job):
import hoomd
from hoomd import md
device=hoomd.device.CPU()
suppress_output_non_root(device.communicator.rank)

cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu, seed=job.sp.seed)
print('start equilibrate')
with job:
    print('starting job')
    # Define constants
    kT1 = job.sp.T1*0.00831446262
    lograte = job.sp.lograte
    print('kT1 defined')
    r_cut = job.sp.r_cut
    p1=job.sp.p1/16.3882464
    equil_time = job.sp.equil_time #10000
    print('r_cut & equil time defined')
    time_step = job.sp.time_step
    print('time step defined')
    sim.create_state_from_gsd(filename=job.fn('lattice_snap.gsd'))
    print('state created from lattice')
    nl = hoomd.md.nlist.Cell(buffer=job.sp.buffer) #BUFFER USED HERE
    integrator = hoomd.md.Integrator(dt=time_step)
    
    lj = hoomd.md.pair.ForceShiftedLJ(nlist=nl, default_r_cut=r_cut)
    
    print('neighborList with buffer, integrator, & lj potential created')
    
    epsilon=job.sp.epsilon; sigma=job.sp.sigma
    
    lj.params[('A', 'A')] = {'epsilon': epsilon, 'sigma': sigma}
    lj.r_cut[('A', 'A')] = r_cut
    lj.params[('A', 'E')] = {'epsilon': epsilon, 'sigma': sigma}
    lj.r_cut[('A', 'E')] = r_cut
    lj.params[('E', 'E')] = {'epsilon': epsilon, 'sigma': sigma}
    lj.r_cut[('E', 'E')] = r_cut
    
    integrator.forces.append(lj)
    print('lj A-A interaction defined & added to integrator')
    
    if job.sp.NPT_equilibrate:
        npt1 = hoomd.md.methods.NPT(kT=kT1, filter=hoomd.filter.All(), tau=job.sp.tau, tauS=job.sp.tauS, couple = 'xyz', box_dof=[True, True, True, False, False, False], S=p1, 
                                    gamma=job.sp.gamma)
        integrator.methods.append(npt1)
    
    else:                         
        NVT = hoomd.md.methods.NVT(filter=hoomd.filter.All(), kT=kT1, tau=job.sp.tau)
        integrator.methods.append(NVT)
    
    sim.operations.integrator = integrator
    print('NPT operation added to integrator, integrator assigned to sim')
    sim.run(0)
        
    _thermodynamic_properties = hoomd.md.compute.ThermodynamicQuantities(filter=hoomd.filter.All())
    sim.operations.computes.append(thermodynamic_properties)
    thermodynamic_properties.loggables
    logger = hoomd.logging.Logger()
    logger.add(thermodynamic_properties, quantities=['kinetic_temperature', 'pressure', 'kinetic_energy', 'potential_energy', 'volume'])
    logger.add(sim, quantities=['timestep', 'walltime'])
    print('logger initialized with timestep and thermo properties')
    
    gsd_writer = hoomd.write.GSD(filename=f"{job.sp.logName}_equil.gsd", trigger=hoomd.trigger.Periodic(lograte), dynamic=job.sp.dynamic, mode='wb')
    
    sim.operations.writers.append(gsd_writer)
    gsd_writer.logger = logger
    #state_writer=hoomd.write.GSD(filename=job.fn('state.gsd'), mode='wb', trigger=hoomd.trigger.Periodic(lograte))
    #sim.operations.writers.append(state_writer)
    print('logger assigned to GSD writer')_
    
    # assign initial velocities
    sim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=kT1)
    
    sim.run(equil_time)
    print("Equilibrating run complete")
    hoomd.write.GSD.write(state=sim.state, filename=job.fn('equilibrate_snap.gsd'), mode='wb')
    print("Equilibrating run written to gsd")
    pass

`

where job.sp.dynamic is ['property', 'momentum', 'particles/typeid']

Thanks in advance!

[joaander]

This is expected behavior. The documentation states:

The dynamic list can contain one or more of the following strings:
...

By inference, this means that no other strings are allowed.

In your case, GSD implicitly considers logged quantities as dynamic and always writes them to the file.

In other words:

• Add the quantity to the Logger to instruct GSD to write a logged quantity.
• Remove the quantity from the Logger to prevent GSD from writing the quantity.

[jackdwwalker]

I see - I had thought that the strings under (for example) the 'property' tag were also viable options for the dynamic list.

Thanks!

[joaander]

I misunderstood. I thought you were asking about quantities defined in your Logger.

'configuration/box', 'particles/N', 'particles/position', ''particles/orientation', ''particles/velocity', ... and similarly documented strings can be provided in the dynamic list to choose dynamic quantities with finer granularity than 'property', 'momentum', etc...

This feature was added in HOOMD-blue 4.0.0. You need to upgrade to use this functionality.