Bonds #41
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Bonds #41
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…ing test script (old_pyMBE.py is just a copy of the current version of pyMBE)
…ionary with the bond parameters and a list of particle pairs
…suite and tutorials
…s in the bond_parameters dict, further corrections in the tutorials and New implementation of the unit test for the define_bond
…check of mandatory use of r_0 in FENE bonds
…nteractions to new behaviour, adapt parameters files
pm-blanco
approved these changes
Apr 23, 2024
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@pinedaps I did some clean-up in the test, adapted the load_interactions functions to take the same arguments as define_bond when reading from file and I fix a bug when defining FENE bonds. It looks good to me know, if you agree with the changes we can proceed and merge this PR. Thank you for your work!
pinedaps
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Apr 23, 2024
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@pm-blanco I just checked your changes and now it looks perfect!
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Fixes #20
List of changes:
The arguments in the function 'create_bond_in_espresso' reduced to two: the string, 'bond_type' and a dictionary, 'bond_parameters' which should contain the parameters for the corresponding 'bond_type', either harmonic or FENE.
Because of the reduction of arguments in the function 'create_bond_in_espresso', the argument of the functions 'define_bond' and define_default_bond' were reduced in the same way. Additionally, now the function 'define_bond' should be called only once by providing a list of the pair of particle types to be bonded in the argument 'particle_pairs'.
All the tests were updated as well as the tutorials.
Finally, the script 'bond_tests.py' is the unit test for checking that all functions involved in the definition of bonds are working properly.