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Fix xtb/docking test#1173

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Commits on Feb 11, 2025

• Skip i==j for avoiding division by zero

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• Skip close atoms for avoiding division by zero as well as avoid complex type transformations

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• Close files properly

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• Cycle after filling gab1/gab2

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• Avoid division by zero by updating expression

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• Use r2 instead of r*r

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