pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:
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 test 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.
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 test 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.