Post-processing modules¶

The list of post-processing modules available directly from .cfg file. Those modules have to be attached to reaction groups.

In the example below, we defined a reaction group abc with three extensions: release_molecule, join_molecule and remove_bond. The name of those extensions have to corresponds to the ext_ sections in the .cfg file. Here, we only show section ext_remove_bond that corresponds to extensions remove_bond.

Every extension section have at least two variables:

ext_type defines the extension type (required)

invoke_on declares on which reactant type the extension will be invoked. The possible options are: type_1, type_2, both (default: both)

Every of the extension section have to set ext_type variable. Other variables in this file are related to the particular extension.

[ext_remove_bond]
ext_type:RemoveNeighboursBonds
bonds_to_remove=C->C:E:1
invoke_on=type_1

[group_abc]
potential:Harmonic
potential_options:K=13622.3,r0=0.256395
extensions:release_molecule,join_molecule,remove_bond

Change neighbour property¶

It allows changing property at certain topological distance from the reacted particle..

ext_type

ChangeNeighboursProperty

type_transfers

The comma separated list of type_transfer definitions. The syntax of single type_transfer: old_type:distance -> new_type(opt1,opt2) where opt1 are optional new parameters of the particle like:

mass: new mass

q: new charge

state: new chemical state

The parameters set here will override the one defined in the topology file.

Remove neighbour bond¶

Remove a bond that is at certain topological distance from the reacted particle.

ext_type: RemoveNeighboursBonds
bonds_to_remove: The comma separated list of bonds_to_remove definitions. The syntax of single bonds_to_remove: anchor_type -> type1:type2:distance where anchor_type is the type of root particle, from where the distance is measured, type1:type2 is the bond to remove (in terms of particle types) at distance.

Release molecule¶

Remove the distance constraint and release a molecule linked to host molecule.

ext_type

ReleaseMolecule

host_type

The type of host particle.

target_type

The type of dummy non-released particle.

eq_length

The distance at which the dummy particle is placed from the host particle.

alpha

The rate constant used to fade in the dummy particle after released.

init_res

The initial resolution of the dummy particle after released.

final_type

The final type of the dummy particle after completely fade in (resolution 1)

cache_file

The cache file for dummy particles (optional)

replicate

How many dummy particles should be attached to a single host particle (default: 1)

release_on

type then the particle will be released whenever the host particle change a type (default)
release_on remove whenever host particle react with other particle

release_count

number of particles to release (default: 1)

Join molecule¶

Add the distance constraint and make invisible one of the particles.

ext_type: JoinMolecule

Freeze regions¶

Define that the box edges will play a role a freeze regions. Whenever a particle of given type reaches this region, it becomes invisible.

ext_type: FreezeRegion

Change randomly particle type¶

Chang randomly particle types during the simulation

ext_type: ChangeParticleType

Simulate ATRP class of the reactions¶

Chang randomly particle types during the simulation

ext_type: ATRPActivator