Fix: Enhance the warning of ntype

[sunliang98]

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Linked Issue

Fix #7229

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[Copilot]

Pull request overview

This PR improves validation and user-facing warnings around ntype by making STRU parsing safer and clarifying how ntype is determined when omitted in INPUT.

Changes:

• Prevent potential out-of-bounds access when checking STRU tokens (temp.empty() guard before indexing).
• Fail fast with a clearer error when no valid ATOMIC_SPECIES entries can be detected in STRU.
• Refine ntype validation: disallow negative values, enforce consistency when explicitly provided, and auto-fill from STRU when ntype == 0.

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