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If a scan is performed over two CVs, or collective variables (bond lengths here), does the code simultaneously step through both of the CVs or does it step through the first one, and scan the second CV at each point of the first CV?

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When you are scanning two bond lengths in Gaussian, you step once through the first bond scan, and complete stepping through the second bond scan. For example, consider the case where you are scanning the bond lengths of C-Cl and C-H in chloromethane. The code will first increment the bond length of C-Cl, and will then scan the C-H bond while keeping C-Cl bond constant. This will result in a 2D scan, with one axis corresponding to C-Cl bond and other corresponding to C-H bond.

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