Correct over-squaring in internal coordinate objective function for adding an atom to XYZ

[alongd]

The objective function for adding a new atom previously led to over-penalization of angular errors (effectively minimizing the error to the fourth power). This was due to the angular constraint functions (g_theta and g_phi) already returning squared errors, which were then squared again in the final objective function.

This commit refactors the constraint functions to return the linear error or linear error magnitude:

• angle_constraint: Now returns the linear difference (calc_angle - target_angle).
• dihedral_constraint: Now returns the magnitude of the sine/cosine error vector (square root of the squared sum).

The main objective function remains structurally the same (sum of squared, scaled terms), but now correctly implements a standard relative squared error minimization.

[Copilot]

Pull Request Overview

This PR fixes an over-squaring issue in the internal coordinate objective function used when adding atoms to XYZ structures. The angular constraint functions were returning squared errors that were then squared again in the objective function, leading to fourth-power minimization instead of the intended squared error minimization.

Key changes:

• Refactored angle_constraint to return linear difference instead of squared error
• Modified dihedral_constraint to return magnitude of error vector instead of squared sum
• Added precision constants to improve code maintainability

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