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Implementation of ABF PES scanning for MM #72

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Commits on Feb 19, 2024

  1. Generalize _read_orca_allxyz to xyz trj and fixed Mayer bond bug

    Modified the function _read_orca_allxyz so that it accepts both "generic"and "orca-flavoured" (with xyz structures separated by ">") xyz multi-structure files.
    
    Also, fixed a bug in reading the Mayer bond order where the letter B was used as a separator to split the various records, leading to crash when the atom name is "Br, Be, Ba" etc...
    mattiafelice-palermo committed Feb 19, 2024
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  2. First implementation of ABF scan

    Modified dihedral_scan.py and forcefield.py to support ABF scan.
    
    Missing features:
     - automatic box sizing
     - automatic determination of # of argon
     - automatic multithread based on atom numbers for ABF run
    mattiafelice-palermo committed Feb 19, 2024
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Commits on Feb 20, 2024

  1. Code clean up

    Removed debug print statements and unused functions.
    
    Increased md runtime for debug purposes.
    mattiafelice-palermo committed Feb 20, 2024
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