Radahn is an interactive molecular dynamic application allowing users to steer their MD simulations and getting live feedback. The framework is currently build around LAMMPS as a simulation backend and will be extended to Gromacs in the future.
Formalize the simulation workflow to integrate thermostats in the simulation.
Thermostats are added in two phases: during a thermalization phase, and the during the equilibration phase.
During the thermalization phase, all the non anchored atom are being affected by a thermostats. During the equilibration phase, only the atoms assigned to a local thermostat are affected.
The interface introduce a new type of jigs: thermostat which can be assigned to atoms the same way anchors are. Local thermostats should be applied around anchors, ideally within a 3 bond radius.
This branch also include a bunch of frontend bug fixes and improvements.
Formalize the simulation workflow to integrate thermostats in the simulation. Thermostats are added in two phases: during a thermalization phase, and the during the equilibration phase. During the thermalization phase, all the non anchored atom are being affected by a thermostats. During the equilibration phase, only the atoms assigned to a local thermostat are affected. The interface introduce a new type of jigs: thermostat which can be assigned to atoms the same way anchors are. Local thermostats should be applied around anchors, ideally within a 3 bond radius.
This branch also include a bunch of frontend bug fixes and improvements.