Atom.java: Enhanced logging when gradient is updated to NaN.
Cluster.groovy: Improved file handling logic.
ForEachFile.groovy: Added verbose logging.
MinimizeCrystals: Created flag to specify minimum iterations to prevent continuous cycling.
SuperposeCrystals: Reorder flags, change distance matrix from TXT to DST.
Barostat.java: Enhance logging when cell parameters are returned as NaN.
SpaceGroupInfo.java: Update CSD population percentages.
Cart2Frac.groovy: Update logging to match paper.
Energy.groovy: Verbose flag and fine logging prints out crystal information for ARC files.
Frac2Cart.groovy Update logging to match paper.
DualTopologyEnergy.java: Fine logging records atoms that are above 0.5Å when using sym op alignment.
ForceFieldEnergy.java: Added fallback for distance calculation if Convex Hull fails (e.g. coplanar molecules).
DistanceMatrixFileFilter.java: Updated matrix files to use DST.
DistanceMatrixFilter.java: Updated comment to reference DST files.
ProgressiveAlignmentOfCrystals.java: Improved z’ handling, sym op print statements, and updated comments.
Superpose.java: Updated distance matrix to DST.
Atom.java: Enhanced logging when gradient is updated to NaN. Cluster.groovy: Improved file handling logic. ForEachFile.groovy: Added verbose logging. MinimizeCrystals: Created flag to specify minimum iterations to prevent continuous cycling. SuperposeCrystals: Reorder flags, change distance matrix from TXT to DST. Barostat.java: Enhance logging when cell parameters are returned as NaN. SpaceGroupInfo.java: Update CSD population percentages. Cart2Frac.groovy: Update logging to match paper. Energy.groovy: Verbose flag and fine logging prints out crystal information for ARC files. Frac2Cart.groovy Update logging to match paper. DualTopologyEnergy.java: Fine logging records atoms that are above 0.5Å when using sym op alignment. ForceFieldEnergy.java: Added fallback for distance calculation if Convex Hull fails (e.g. coplanar molecules). DistanceMatrixFileFilter.java: Updated matrix files to use DST. DistanceMatrixFilter.java: Updated comment to reference DST files. ProgressiveAlignmentOfCrystals.java: Improved z’ handling, sym op print statements, and updated comments. Superpose.java: Updated distance matrix to DST.