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To your question - just call run 1000, then displace_atoms, then again run 'whatever_you_need'.
Please also keep in mind that "velocity set" is an instantaneous command just like displace_atoms, it will not by itself keep velocity zero for the whole calculation. To keep atoms fixed, do not include them in time integration.
16.04.2014, 20:28, "prashant gupta" <[email protected]>: