Changes

1. io: new function read_lattice_extxyz 87f2e77
2. utils: new method par_rebond for rebond all molecules in parallel 669d57f
3. Molecule: new method has_bond 2605f8f
4. Molecule: new method from_json for deserialize from to_json 1a9a8cf

Changes

• lattice: add new clone method 48abc68
• rebond: allow set distance cutoff for nearest neighbors 134d964
• rebond: support vmd scheme with param bond_scale_factor 231b4b6
• rebond: add parameter cov_radius_scale_factor 78a4dd7
• remove rebond parameter from view_in_pymol fa89f97
• do not rebond in view_in_agui e46cc1f
• rebond in multiwfn scheme based covalent radii sum 03485f4

1. chemenv: Preliminary implementation of variable cell optimization (need to be improved)
2. Molecule: Add set_lattice_scaled method, which automatically scales the atomic coordinates when set new cell.
3. analysis: Add new mthod for creating chemical bonds from bond valences based on kmeans clustering algorithm (rebond)
4. analysis: Automatically set missing parameters such as max_atom_valence, max_coordination_numbers, etc. when evaluat/rebond

Fix an issue in BondValenceModel with user defined Options

New features

• Molecule: Add methods to read or set atom label (get_atom_label, set_atom_label)
• Add analysis module used for CN, GAV and other properties based on bond valence model

• gosh: optimize using custom calculator
• support python 3.8
• fix panic issue in utils.set_verbosity

New features:

• Add gui module for molecule visualization
• add view function for view molecule using gchemol-view

Changes:

• [2023-04-29] Molecule: improved fingerprint method to be uniq for different atom kinds or diffent bond kinds.
• [2023-04-29] Molecule: new symbols and atomic_numbers methods
• [2023-04-20] Added functions for visualization of molecules using jmol/agui
• [2023-04-20] Added spdkit-view script for easy viewing of molecular files

• view_in_pymol: allow view molecules on a remote server based on rpyc.
• Molecule: Add format_as method to format molecules directly as strings.
• Fixed minijinja's issue on scientific notation of floating point numbers (minijinja 0.30.6+).
• Molecule: Add selection_freezed_atoms method for viewing fixed atoms.

• surface: new function fragment_atoms_by_layer for finding atoms layer by layer in slab model
• Molecule: rebond now allow set bond_tolerance parameter
• Molecule: new connected_fragment_atoms method for finding atom fragment containing specfic atom
• Molecule: support .xsd and .car file types, and read freezing atoms data from .xsd file
• Lattice: new methods scale_by_a, scale_by_b, scale_by_c for scaling lattice size in different direrctions