Fix and optimize get_S sparse output

[sgyang345]

Reminder

• I have read AGENTS.md and docs/developers_guide/agent_governance.md.
• I have linked an issue or explained why this PR does not need one.
• I have added adequate unit tests and/or case tests, or explained why not.
• I have listed the exact verification commands run and their results.
• I have described user-visible behavior changes, including INPUT parameter changes.
• I have explained core-module impact for ESolver, HSolver, ElecState, Hamilt, Operator, Psi, or other source/ changes.
• I have requested any needed governance exception below.

Linked Issue

Fix #

Unit Tests and/or Case Tests for my changes

• Commands run:
• Result summary:
• Checks not run, with reason:

What's changed?

• Example: brief summary of the user-visible or developer-facing change.

Governance Notes

• INPUT/docs changes:
• Core module impact:
• Exceptions requested: