Update #2
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Update #2
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Added get_msd_from_dump function. Currently only supports msd calculation for entire system (not for individual molecular species). Can calculate msd based on positions for all atoms or CoM positions for all molecules.
Bug fixes.
Changes the way rdf_partial works: uses separate atoms types for each atom in a molecule rather than using lammps atom types
I tested this on 401 frames with 10479 atoms total and the run time was 1.5 seconds/file giving a speed enhancement of more than 300 times compared to the original. Note: after adding the Numba function, I noticed there are some differences in the values calculated as compared to Maxim's original code, but will check what is causing this and edit it accordingly.
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Various bug fixes and adding Maxim's new rdf code