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Structure relaxation

In general, the atom configuration made systematically using mkconf_* may not be most stable structure and one needs to relax the structure. To relax the strucure, you can run MD simulation with velocity damping as,

  • without controlling temperature ( temperature_control to be none);
  • with applying velocity damping ( flag_damping to be 1 to use velocity damping);
  • with convergence criterion 1.0e-4 eV ( converge_eps to be 1.0d-4 ).

Then atoms move towards the direction where the forces on atoms indicate with reducing their energies, and finally the system becomes the minimum energy structure.

After relaxing the structure with some outputs, use the relaxed structure as the initial structure of the next simulation as,

mv pmdini pmdorig     <== save initial structure to pmdini
mv pmdfin pmdini      <== replace pmdini with pmdfin (relaxed structure)