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33 ppstm simple to functions #36

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33 ppstm simple to functions #36

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LauriKurki
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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
moved test scripts from root to specific folders
361fa5d
@LauriKurki
cut_eigenenergies takes cutoff voltages as arguments instead of using…
d3b0e81 
… global variables
@LauriKurki
added function read_dft to read eigenenergies and coefficients
e6bd3a8
@LauriKurki
added module STMutils
5dda09b 
Functions:
  - tip orbital coefficients based on the tip
  - get tip positions for fixed or relaxed scan
  - run_stm_scan (does the scanning)
@LauriKurki
added module visualization for creating the outputs
3286973
@LauriKurki
added ppstm_run.py to replace PPSTM_simple.py
7a3fcfd 
This file takes a config file as command line argument and runs the stm scan using the settings
@LauriKurki
Added default config with descriptions for each option
116182f
@LauriKurki
removed debug prints
837c755
@LauriKurki
4N coronene tests now use the new config file system
f26b4b6
@LauriKurki
deleted duplicate scripts and link to the repo
5d26e03 
Also changed relative location of the repository root.
Same will be done for other tests next.
@LauriKurki
fix for npz file naming
e4b06df
@LauriKurki
fix for fixed tip position initialization
168abe6
@LauriKurki
updated cupc tests
6dd9064
@LauriKurki
updated cupc tests
d4c7447
@LauriKurki
updated FePc tests
ec198de
@LauriKurki
updated orbitals tests
46c655d
@LauriKurki
removed linked ppstm from orbitals-test
7aa96c1
@LauriKurki
updated ptcda_mol tests
a09efd9
@LauriKurki
updated Si_7x7 tests
c18b3ff
@LauriKurki
updated TOAT tests
70627af
@LauriKurki
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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

@LauriKurki LauriKurki marked this pull request as ready for review September 30, 2024 14:56
@ondrejkrejci
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I had forget about this - is this an active one? Sorry.

ondrejkrejci
ondrejkrejci requested changes Mar 4, 2025
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Thank you, looks very good, comments in the files themselves. Sorry for my delay!

pyPPSTM/ReadSTM.py
@@ -201,18 +203,16 @@ def to_fermi(eig, fermi, orig_fermi=0.0):
eig -= fermi
return eig;

def cut_eigenenergies(eig):
def cut_eigenenergies(eig, cut_min, cut_max):
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While, I am definitely for this one, I do not see, that the you would remove the global definitions at line 102 and 103. Would it be possible to remove them? If not, please add a comment so they should be removed in the future.

ppstm_run.py

if __name__=='__main__':
# Get config file from command line
config_file = sys.argv[1]
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Could you please add here a helper message, if there is no argv, or more than 1, thank you!

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@ondrejkrejci ondrejkrejci ondrejkrejci requested changes

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@LauriKurki @ondrejkrejci