Releases · cmelab/msibi

State and Pair API changes:

Creating a State object will automatically handle the creation of a states directory and a corresponding directory for each state.
The add_state function of pair.py now has a calculate_target_rdf option, so that the target RDF can be determined from the trajectory passed into the State object. The user can still manually pass into target_rdf (either a text file or np array).
The MSIBI object that is created first gets passed into each State created. This is to ensure that the rdf related parameters are available when using calculate_target_rdf=True . I couldn't really think of a better way to do this.
Added calcualte_rdf.py to the utils dir. This has a function called state_pair_rdf using freud (via cmeutils). This is what is used when calcualte_target_rdf=True in Pair.add_state() This function could probably just be moved into state.py. I wasn't sure if there would be more involved that might warrant having an rdf related file in utils

Other changes:

The hoomd system loaded in the HOOMD2_HEADER starts from frame 0 of the trajectory rather than the last frame.
The same rdf function above is used in the compute_current_rdf() function during iterations.
Freud used for RDFs instead of mdtraj

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