Bug Description

See #1939 for more details. Whenever we significantly change RMG-database, the comments in the chemkin file need to be updated or else this uncertainty IPython notebook example will be broken. It is not ideal to continually update this file, so we should come up with a better solution. Possibilities include:

1. Only update this file every major release. Add a note in the IP

The Poisson solve absolute tolerance sets the accuracy of the Poisson solve. Given the value of abs_tol, the error level targeted in the Poisson solve is abs_tol * 4 * pi * G * rho_max, where rho_max is the maximum density on the domain. For Cartesian simulations the default value is 1.e-11, and for non-Cartesian the default value is 1.e-10.

At high resolution, and/or for complicated mass distr

Running the EA examples should be part of the CI

actually : form('myForm')

may be later : form(action)

As mentioned in #27, the core.database method to assign a reaction role id needs a rework, along with possibly a change in the DB tables. A migration script would most likely be necessary in that case.

ARC should search CCCBDB to scrap geometries, if available, before generating conformers. Usually, the species on CCCBDB are relatively "small", so this is not so much to improve the chances of getting the correct conformer but to increase the efficiency by reducing the number of spawned jobs (several conformers are run and compared per species).