Review settings names

[IAlibay]

We should review our settings name & change things ahead of the 1.0 release.

[hannahbaumann]

From discussion from this weeks power hour:

• AlchemicalSamplerSettings:

• Potentially make 3 subclasses for different samplers.

• Rename flatness_criteria to sams_flatness_criteria and gamma0 to sams_gamma0

• rename

  • online_analysis_interval to real_time_analysis_interval,
  • online_analysis_minimum_iterations to real_time_analysis_minimum_iterations,
  • online_analysis_target_error to early_termination_target_error

• Change doc string of online_analysis_target_error to make it clear how the error is calculated and that the ERROR has to be below this value, not the free energy as currently stated

• Move n_repeats upstream (Protocol settings)

• In plain MD protocol, move n_repeats from RepeatSettings to protocol settings?

• Potentially combine AlchemicalSamplerSettings with SimulationSettings.

[hannahbaumann]

• AlchemicalSettings:

• remove flatten_torsions

• rename interpolate_old_and_new_14s to turn_off_core_unique_exceptions

• change doc string for interpolate_old_and_new_14s

• Move lambda_functions and lambda_windows to different LambdaSettings class.

• rename softcore_LJ_v2 to softcore_LJ and unse literal 'gapsys' instead of True/False

• rename unsampled_endstates (ideas: sample_non_alchemical_endstates True/False, or endstate_correction )and rewrite the doc string to make it clear what the setting does (decision: endstate_dispersion_correction)

• Move use_dispersion_correction to where PME stuff is (or ForceFieldSettings?)

[hannahbaumann]

• ForceFieldSettings:

• add doc string for rigid_water and remove_com

• Move remove_com to IntegratorSettings?

[hannahbaumann]

• IntegratorSettings:

• rename n_steps to steps_per_iteration

• Move steps_per_iteration to AlchemicalSamplerSettings

[hannahbaumann]

• SimulationSettings:

• Potentially combine SimulationSettings and AlchemicalSamplerSettings

• Move settings that are only related to outputs (e.g. output_filename) to an OutputSettings.

[hannahbaumann]

• SystemSettings:

• Merge SytemSettings to ForceFieldSettings

• Rename nonbonded_method, maybe two separate entries for LJ and Coulomb?

[hannahbaumann]

Diagram for new (in progress) settings updates:
https://drive.google.com/file/d/1tsNU9WkAihFPDIsR_zB8sE3zRt5h_NiR/view?usp=sharing