Planned features

[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 features

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

Basic features

• natoms
• concentration
• box
• atoms
• add_atoms
• repeat
• read_file
• to_file
• to_ase
• extract cubic box
• show (Add viz #16)
• custom lattice creation (add custom lattice creation pyscal#138)
• Rotation
• Slicing
• GBs (Improve gb #17 )

Neighbor methods

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

Steinhardt

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

Solid

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

Misc

• RDF (Rdf pyscal#124 )
• Angular criteria (Angular pyscal#125 )
• Chi params (Angular pyscal#125 )
• SRO (Add sro #14)
• PMSRO (Add sro #14)
• Entropy
• energy
• Diamond neighbors (Add diamond neighbors #4 )
• CNA (Add cna #3 )
• Adaptive CNA (Add cna #3 )
• Identify diamond neighbors (Add diamond neighbors #4 )
• Centrosymmetry (Add centrosymmetry #5 )
• Vorovector (Vorovector #13 )
• Space group, point group calculation (Add symmetry pyscal#137 )

Other modules

• Traj process
• crystal structures
• Trajectory (add tests and example for trajectory #31)

Others

• Update docstrings
• calculation of w parameters pyscal#22
• find_solids and calculate_q incompatible pyscal#101
• Change documentation  pyscal#105
• Calculations should throw error if neighbors are not calculated pyscal#108
• Ghost atoms appear in neighbors pyscal#110 (replace ghost atom indices with real ones #30 )
• Calculation of SRO for multicomponent systems pyscal#111