Re-implement DFT-D3 against the s-dftd3 reference

[Growl1234]

Note

This PR is based on #7810 as they share the same input parameters settings. Please merge #7810 first.

This PR re-implements the internal DFT-D3 module with s-dftd3 as the reference, while keeping the implementation fully ABACUS-native without introducing an external s-dftd3 dependency.

The legacy D3 evaluator and manually maintained parameter tables are replaced with a substantially simplified implementation that:

• separates the ABACUS-facing Vdwd3 wrapper from the standalone D3 numerical evaluator, so vdwd3.cpp now mainly handles input, structure adaptation, and unit conversion, while vdwd3_evaluator.cpp contains the actual D3 model;
• follows the s-dftd3 reference model for coordination numbers, C6 interpolation, D3(0), D3(BJ), and ATM;
• uses a single evaluator for energy, forces, and virial instead of maintaining separate energy and derivative code paths;
• generates reference data and damping parameters from a pinned s-dftd3 version;
• separates coordination-number, two-body, and three-body cutoffs, with smooth-cutoff support;
• simplifies periodic image handling and analytic derivative evaluation;
• introduces shared vdW XC-name normalization for D3 and D4;
• preserves automatic XC detection and user parameter overrides.

The new implementation is validated against s-dftd3 reference energies for molecular, periodic, zero-damping, BJ-damping, ATM, and actinide cases, together with finite-difference checks for gradients and virials.

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