Make number of removed DOF optional

[joaander]

Original report by me.

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HOOMD integrators assume that momentum is conserved in PBC, and there are always N_dimensions DOF removed from the system for temperature computation. This assumption is not always valid, as the user can create systems where momentum is not conserved (i.e. integrated particles bonded to pinned particles). The user should have an option to remove these DOF or not.

The relevant code to modify is:

IntegratorTwoStep::getNDOF
return res - m_sysdef->getNDimensions() - getNDOFRemoved();

[joaander]

It seemed like a good idea at the time, now I don't see the use-case for this.