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added 15 commits
March 16, 2021 14:36
Commit as about to cut up some code Theory appears working at this point Breadth first search code presumed unnessary here
About to remove the switch search order system Needs replacing with something less goofy and more robust
Path search correctly maps all the atoms it's designed for in DGEBA test To be expanded to produce clear output for further testing
More testing examples included and clearer format Path search can now handle missing atoms - first version at least Turned off for now until symmetry solving is built
Partial structure finders now calculate edge atom fingerprints These are stored as comments at the top of the file These are used for during the mapping process
LammpsBondReact can now be used in terminal Includes optional args and error checks Fixed get_data exception handling after I broke it Partial file creators add edge fingerprints properly Folder tidied up to remove old code
BondingAtoms are now read from the molecule files for path search LammpsToMolecule changed to require bond atoms from the user
Path Search can now consider edge atom fingerprints. DGEBA tests show this working successfully. Fingerprints have been adjusted to not include AtomIDs Tests have been cleaned up - more to come
Designed to get neighbours of neighbouring atoms Slightly overcomplicated implementation, going to simplify
Map can now solve symmetric atoms by looking at first neighbours Various rejigging of the path search has been done Test created for finding neighbours at different distances
Path search passes all current tests in MapTesting Added symmetry atom negotiation for missing atoms More unit testing, map testing and commenting to come Need to expand compare_symmetric_atoms to include additional tests
Path search can now loop through missing and queue. This means atoms bound to a missing atom can be found normally Unit test created for find_partial_structure
map_path_search can now output map files DeleteIDs now handled at all levels Update required for partials to include deleteIDs as standard
PathSearch can handle symmetric atoms and infer Detailed path info available by logger Testing updated to relative pathing and is working Delete atoms added as potential user input Tidy up of repo, mainly testing
General tidy up and minor changes to code Documentation improved Example workflow provided - to be changed later
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The beta version of AutoMapper built with an adapted path search is complete.