dybond¶

snap_simulate.hoomd.simulation.build_dybond(Dybond, snap, dt, seed, hoomd_objs)[source]¶

This function parses the dybond block to configure dynamic bonding constraints.

Warning

The custom hoomd.dybond package must be installed in the simulation environment for these dynamic bonding options to run correctly. See the DyBond-v2 repository for installation and details.

nlist: "cell"               # Reference to a neighbor list defined in nlist (required)
thermo: "thermo"            # Reference to a compute defined in computes (required)
trigger: 100                # Updater trigger (required: integer period or trigger name)
nearestNeighbor: true       # (Optional, default True)
specs:
  patch_linker:
    pair: ["patch", "linker_end"]
    bond: "Harmonic"        # Reference to a bond defined in bonds (required)
    bond_typename: "patch-linker_end" # (Required unless bond_typeid is used)
    # bond_typeid: 2        # (Alternative to bond_typename; mutually exclusive)
    kon: 1.0                # Reaction rate for bond formation (required unless Pon is used)
    koff: 0.1               # Reaction rate for bond breaking (required unless deduced via epsilon)
    rmin: 0.7               # Minimum distance for bond formation (required)
    rmax: 1.2               # Maximum distance for bond formation/breaking (required)
    selfAvoidFlag: true     # (Required) Exclude same-molecule bonds

    # Optional metropolis criteria for bond formation (default True)
    metropolisFlag: true

    # Optional force dependence parameter for bond breaking (default off)
    force_a: 1.0

    # Optional bond melting parameters (default off)
    Tmelt: 1.0
    alpha: 200.0
    kon_melt: 1.0
    koff_melt: 20.0

Note

Bond potential parameters (such as spring constant \(k\) and equilibrium bond length \(r_0\)) are not specified in dybond; they are inherited directly from the referenced bond potential defined in the bonds block.
Dynamic bonding features configure the custom hoomd.dybond extension. Refer to the DyBond-v2 repository or research publications for exact scientific parameters.