GitLab

Update from upstream

Signature modification to Modeller.addExtraParticles()

Within Modeller.addExtraParticles(), add the ability to pass down
an option to modify compiled.matchResidueToTemplate() 's
ignoreExternalBonds parameter.

https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=11264&p=0&start=0&view=&sid=e384beeb08f3bfd767dcfb546006ad63

Optimized processing of expressions with tabulated functions

ThreeParticleAverageSite Doxygen fix #2473

Update travis to test more recent Python versions

runForClockTime() updates currentStep correctly

Get and scale velocities using numpy during simulated tempering

Improved determination of elements from Gromacs top files

Prevent memory from exploding when particles get too spread out

Fixed errors with Doxygen 1.8.16

Allow multiple matching templates if they assign identical parameters

make std::string pass as references, not values

Fixes _addIons behavior for membrane systems.

Avoid unnecessary force evaluation when computing kinetic energy

Restraint existing atoms during addHydrogens

Create BAOABLangevinIntegrator

Catch exception when cl::Platform::get() fails.

make non-primitave types pre increment instead of post increment