Adding new bonds and angles with custom updater

[nmendiboure]

Hello !

I'm currently trying to create a new bond between 2 beads of 2 different polymers if they are close by a certain distance. I'm using a Custom.Action class and the snap = self._state.get_snapshot() function. But when I want to add new bond groups, or new bond typeid, or even angles groups, it simply says:

AttributeError: property of 'BondDataSnapshot' object has no setter

As I understand it, I can only modify existing elements, but not add new ones...

Am I missing something that would allow me to define new bonds and angles, or do I need to convert my snapshot to a gsd snapshot and start a new simulation from there?

def update_snapshot_data(snapshot_data, new_groups, new_typeids):

    number_of_entries = len(new_groups)

    groups = snapshot_data.group if snapshot_data.N else []
    groups = list(groups) + list(new_groups)
    snapshot_data.group = np.asarray(groups, dtype=np.uint32)

    typeids = snapshot_data.typeid if snapshot_data.N else []
    typeids = list(typeids) + list(new_typeids)
    snapshot_data.typeid = np.asarray(typeids, dtype=np.uint32)

    snapshot_data.N += number_of_entries

Thanks in advance

[joaander]

HOOMD's snapshot data structure is not Pythonic - it is a thin wrapper around a C++ data structure. You cannot overwrite the .group attribute because it is managed by C++.

To expand the group array, first set the new N:

snapshot_data.N += number_of_entries

Now the snapshot_data.group array is larger and you can write to its contents with:

snapshot_data.group[:] = np.asarray(groups, dtype=np.uint32)

[nmendiboure]

Hi thanks for the answer.

I managed to handle that by converting my hoomd.Snapshot object into a gsd.Frame. I then modified the gsd file, converted it back into a Snapshot, and applied the changes using self._state.set_snapshot(snap). It seems to work well.

I saw that there was a function to convert a gsd into a Snapshot : hoomd.Snapshot.from_gsd_frame(gsd, communicator) , but I didn't find one to do the opposite, so here mine :

def snap_to_gsd(snap):
    snap_gsd = gsd.hoomd.Frame()
    for attr in snap_gsd.__dict__:
        data_gsd = getattr(snap_gsd, attr)

        if hasattr(snap, attr):
            data = getattr(snap, attr)

            if hasattr(data_gsd, '__dict__'):
                for prop in data_gsd.__dict__:
                    if hasattr(data, prop):
                        setattr(data_gsd, prop, getattr(data, prop))
                    elif hasattr(data, f"{prop.lstrip('_')}"):
                        # If a private attribute, get it with leading underscore
                        setattr(data_gsd, prop, getattr(data, f"{prop.lstrip('_')}"))

    return snap_gsd

[joaander]

I would also welcome contributions that add a Python API to create particles/bonds/dihedrals/etc.. See the proposal in #1535.