reactions

Bug Description

There is a wrong input at Example Input Files at RMG User's Guide (https://react

castro.change_max = 1.0 means that the timestep can only ever stay the same or decrease relative to its initial value. I think we should disallow this value, I have a hard time imagining a use case for this (if you want a fixed timestep, use fixed_dt, and if you want a timestep cap but still allow the timestep to decrease, use max_dt). It causes problems with the retry functionality.

In the file defining the Alkene functional group (stk.molecular.functional_groups.alkene.py), lines 103 and 116 return self.atom1 and self.atom2.
atom1 and atom2 do not exist.
Should be return self._atom1 and return self._atom2.

This issue is not picked up with the current tests so suggests a need to see if each atom can be retrieved successfully ( get_carbon1 etc.) for each fu

Is your feature request related to a problem? Please describe.
When running many species / reaction in ARC, it is often helpful to trace the history of a single species or TS. THe current log file is too large to do that conveniently.

Describe the solution you'd like
Create a log file in the output folder of each species / TS with the relevant data.

In beam experiments often the delay between species creation and diffusion to the detector is modeled as a constant TP domain with a first order loss outlet. The first order loss outlet molar flow rate is some constant loss rate k times the moles in the constant TP reactor. Some of our users have requested this feature.

actually : form('myForm')

may be later : form(action)