Remove atoms from base calculator

From IRL discussions we agreed to move the responsibility of the actual configuration being sampled on from BaseCalculator to ConfigurationManager.

The reason for this is that the current design made it awkward to set elements etc since both the configuration in the Calculator and the representation in configuration manager needed to both be updated.

Keeping the configuration information in one place makes things more maintainable and possibly less bug-prone.

Tasks

  • remove atoms from calculator
  • put atoms to configuration manager
  • solve any issues that arises
  • Code and docstrings is understandable
Edited by Mattias Ångqvist
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