33 ppstm simple to functions

[LauriKurki]

This is a rather large PR with a lot of changes

• add modules pyPPSTM/STMutils.py and pyPPSTM/visualization.py that contain all the functionalities previously in PPSTM_simple.py
• STM settings are now read from a .toml file
• add script run_ppstm.py that uses the functions from the above modules
  1. read settings
  2. get tip orbital coefficients
  3. read eigenenergies and coefficients
  4. (optional) read input_plot.xyz
  5. get/calculate tip positions
  6. run scan
  7. output
• update all the tests by removing duplicate scripts

[LauriKurki]

I'm done with the updates now. All the tests have .toml files, and the run_tests.sh scripts for each test case have been updated correspondingly. I checked that all the tests run, but could you @ondrejkrejci also check if there's something that should be checked?

For now, the script is run with a command like this

python $PPSTM_PATH/ppstm_run.py config.toml

and there's a default/example config in configs/default.toml.

TODO:

• documentation for the script (I will do this after the cli update Code reorganization #34 )
• at the moment, the code requires all the config options to be defined in the configuration file. This should be changed so that user can only define what they really want, and otherwise use default parameters