add user guide, update configs, data_collator and tokenizer

[a-kore]

Feature

Short Description

• Improve documentation for data_collator and fix masking functionality
• Update tokenization scheme and add extra tokens from Atom3D datasets.
• Create utils.py in data module and add metrics computation for Atom3D tasks.
• Fix bugs in model configs.
• Add AtomFormerForSystemClassification to facilitate classification/regression tasks on Atom3D tasks.
• Update index.md and user_guide.md.
• Add run_atom3d.py to faciliate fine-tuning on atom3d tasks with pre-trained models.