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Feat: Implement constrained optimization via Null-Space Projection with `-pc` flag

- Introduce `CRSIRFO` optimizer for rigorous constraint handling using SVD-based projection.
- Implement SHAKE-like coordinate correction and Hessian-based gradient transport to maintain manifold consistency.
- Delegate convergence check to the optimizer to handle residual constraint forces (tension) correctly.

Usage:
  python optmain.py <input> -opt crsirfo_block_fsb -pc bond 1,2 angle 1,2,3 dihedral 1,2,3,4

Command Details:
  -opt crsirfo_block_fsb : Selects the projection-aware RS-I-RFO optimizer.
  -pc bond 1,2           : Constrains the distance between atom 1 and 2.
  -pc angle 1,2,3        : Constrains the bond angle of atoms 1-2-3.
  -pc dihedral 1,2,3,4   : Constrains the torsion angle of atoms 1-2-3-4.

 - fix a small bug (calc_tools.py)

Author: ss0832