feat: enable batch processing of multi-structure .xyz files with 3D array to Z-matrix

[OiChihang]

Hello, I am glad to join in this repo.

• Add xyzcounter to count structures and atom numbers
• Refactor readxyz to return 3D numpy array [nstruct, npart, 3]
• Refactor write_zmat to output Z-matrix for all configurations
• Update distance_matrix to handle both 2D and 3D arrays
• Increase float precision to 8 decimal places in write_zmat routine

Have a good day.