211206 rMD dev Meeting Protocol

[ehhartmann]

• write sequence of tasks in yaml file with single and recurring tasks, the task queue is built from that
• recurring tasks that are ordered in a recurring tasks group have a mult variable associated with the group that denotes how often the group of tasks is repeated
• a task is allowed to build an inner task queue if subsequent tasks are necessary
• a global step variable with be used to count and limit the overall number of tasks (including inner tasks)
• no other counting variables should be used as of now, this may change later
• functions should have a documentation string
• the reaction recipe should be attached to all generated rates
• atomtypes should not be part of the reaction recipe
• reactions is a ABC and should not contain functions that are useful for all reaction classes, these can be stored in the utils file

[jmbuhr]

For future reference: All current examples are run with a plumed-patched gromacs 2021 version compiled by @ehhartmann which can be enabled by source /hits/fast/mbm/hartmaec/sw/gromacs-2021/run/bin/GMXRC