Create a class to manage simulation inputs

[yakutovicha]

Currently, all the input parameters are stored in the params variable of the common.py module. The problem with this approach is that there is only one instance of the module, so one cannot keep running multiple simulations as they might require different inputs.

So, I suggest migrating input configuration into a class and handling things there.

Ideally, after this is implemented the test tests/_test_vdw.py can be re-enabled and everything should pass.

• Move the default params.ini file from the ppafm/defaults/ folder to the wiki to give people an idea of what it looks like.