Implement manual trigger of bond breakage (for use with Lees-Edwards)

[RudolfWeeber]

• The breakable bonds feature removes bonds stretched beyond a certain limit.
• The breaking happens during the integration loop, after the force calculation
• Under normal conditions, no bonds exist with a length beyond the breakage limit after the integration has finished
• But when Lees-Edwards (LE) boundary conditions are active, the shift across the periodic boundary changes, as the time step is advanced. In this way, bound particles interacting across the periodic boundaries can be separated by more than the bond length in rare cases.

@bindgens1

Temporary "solution": rewind the LE offset change applied in the last time step before stress measurement, measure stress, re-apply LE offset.

The proper solution is to introduce a script interface call to manually trigger the bond breakage. I'd hesitate to put this into the analysis routines, because analysis shouldn't actually modify the system.

Steps

Core

• In src/core/bond_breakage/bond_breakage.{cpp,hpp}:
  • Write a bond handler which, if it gets a pair bond, evaluates the bond breakage criterion.
    • This can be a copy of the first few lines of forces_inline.hpp::add_bonded_force()
  • Write an execute_bond_breakage() function
    • Call the method to clear the bond breakage queue
    • Use CellStructure::bond_loop with the bond kernel from the previous step (cf short_range_loop.hpp)
    • Run the method to process the breakage queue

Script interface

• Create src/script_interface/bond_breakage/BondBreakage.hpp as an instance of AutoParameters.
  • See src/script_interface/particle_data/Poymer.{hpp,cpp} as template
  • The constructor can be left empty (or omitted)
  • Only the do_call_method() has to be implemented
  • Add a single method called "execute", calling the execute_bond_breakage() method written in the core
  • Register the BondBreakage script interface class in src/script_interface/bond_breakage/initialize.cpp
  • Add the BondBreakage.cpp file to the CMakeList.txt

Python

• Make the BondBreakage script interface class known to python.
  • Cf the Union class in shapes.py
  • Only the _so_name and _bind_methods are needed

[RudolfWeeber]

See the test case testsuite/python/bond_breakage.py

And the doc of the feature: https://espressomd.github.io/doc/advanced_methods.html#deleting-bonds-when-particles-are-pulled-apart

[RudolfWeeber]

This ticket is suitable for early/new contributors, when it comes to the core implementation. An experienced dev can help with the script interface bindings.

[RudolfWeeber]

@bindgens1 Is this still needed. As far as I understnad, the crashes were caused by sth else?

[bindgens1]

@RudolfWeeber I could run my simulations in the end, but I still think that this is needed in features that utilize Lees-Edwards. I do not need it for my specific use case.