Version 3

[srmnitc]

This version enables a major restructure of code. The key ideas behind the restructure of the code base are:

• Reduce the memory used by pyscal. Currently atom objects are C++ based. There are always copied for each calculation. The atom objects should be removed, and replaced with a Python object so that it can be directly interacted with.
• Reduce C++ code. To easily maintain the code, C++ side should be reduced to a set of methods for the time critical parts. The rest of the code should be on the python side.

Check list for merge

• full Atom rewrite (Update atom backend #135 )
• Separate operations into invidual classes (prototype Separate operations #136 )
• Full system rewrite

Basic features

• natoms
• concentration
• box
• atoms
• add_atoms
• repeat
• read_file
• to_file
• to_ase
• extract cubic box
• show
• custom lattice creation (add custom lattice creation #138)
• Rotation
• Slicing
• GBs

Neighbor methods

• Cutoff
• adaptive
• SANN
• Number
• Voronoi (initial draft of voronoi #127 )
• Mask (Mask #118, Mask #119 )
• Filter (Mask #118 )

Steinhardt

• Normal (Mask #119, update plm implementation #121)
• Averaged (add averaged keyword #117, Mask #119, update plm implementation #121)
• Disorder (Disorder #122 )

Solid

• Solid identification (Solids #123 )
• clustering (Solids #123 )
• largest cluster (Solids #123 )

Misc

• RDF (Rdf #124 )
• Angular criteria (Angular #125 )
• Chi params (Angular #125 )
• SRO
• PMSRO
• Entropy
• energy
• Diamond neighbors
• CNA
• Adaptive CNA
• Identify diamond neighbors
• Centrsymmetry
• Vorovector
• Space group, point group calculation (Add symmetry #137 )

Other modules

• Traj process
• crystal structures
• Trajectory

Others

• Update docstrings
• calculation of w parameters #22
• find_solids and calculate_q incompatible #101
• Change documentation  #105
• Calculations should throw error if neighbors are not calculated #108
• Ghost atoms appear in neighbors #110
• Calculation of SRO for multicomponent systems #111