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Confusing behavior of ThermodynamicState system attribute

See original GitHub issue

@andrrizzi : Any idea what is going on here?

Let’s check how many torsion terms there are:

>>> from openmmtools import testsystems, states
>>> from simtk import unit, openmm
>>> testsystem = testsystems.HostGuestVacuum()
>>> testsystem.system.getForce(2).getNumTorsions()

Now what happens if we create a ThermodynamicState?

>>> thermodynamic_state = states.ThermodynamicState(testsystem.system, temperature=300.0*unit.kelvin)
>>> thermodynamic_state.system.getForce(2).getNumTorsions()

Huh? But it gets weirder:

>>> system = thermodynamic_state.system
>>> system.getForce(2).getNumTorsions()

Is accessing a method of thermodynamic_state.system somehow causing @setter instead of @property to be called?

Issue Analytics

  • State:open
  • Created 6 years ago
  • Comments:7 (6 by maintainers)

github_iconTop GitHub Comments

andrrizzicommented, Dec 5, 2017

Ah! This is likely caused by how the SWIG memory is handled. thermodynamic_state.system is a copy. If you don’t assign it to anything, the garbage collector is going to pick it up as soon as it has the chance. The force returned by thermodynamic_state.system.getForce(i) does not own the SWIG C++ memory, so the System gets deallocated, and by the time you call getNumTorsions(), that area of the memory could be already overwritten. I’m surprised you didn’t get a segfault.

jchoderacommented, Dec 6, 2017


Also, their sphinx docs stylesheet is gorgeous!

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