Dear Reza, Exploring the potential energy surface of glassy systems is not a trivial problem not to mention impurities in glassy systems. Depending on how deep you want to explore this, you may want to explore PLUMED package which is compatible with PWscf.
http://www.plumed-code.org/ For something quick, I would run an MD at very high temperature , take 100 snapshots from the run , and relax them at zero temperature. Regards, Mostafa MIT
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