#!/bin/sh # In this example of green, the self-energies are calculated of gold electrodes, # the material most often used in molecular electronics. # In the example for the Benzenedithiol junction, green_BDT.run, these self-energies # will be used to calculate the DOS and transmission of a benzenedithiol junction. # Each principal layer contains 3x3x3=27 gold atoms. # For the calculation of the self-energies three principal layers are needed, # and therefore 81 gold atoms in total. # To keep the runtimes manageable it is therefore important to choose the basis set # as small as possible. # For transport calculations, a DZ basis with a large frozen core is generally sufficient. # Unfortunately, even with the largest frozen core (Au.4f), # the basis set for Au still contains 19 electrons. # A significant speedup can be obtained by limiting this to 11 electrons # (only the outer *d* and *s* shells). # Be advised that even with this reduction the total runtime of calculation can be long. # To facilitate the calculation of the electrodes, # first a gold atom fragment will be calculated with the smallest possible basis. # The sample directory contains the required Au.5p and Au.5p.dirac files. # Note that for gold relativistic effects are important. # Therefore Scalar ZORA will be used throughout this example. cp $AMSHOME/examples/adf/green_Al/Au.5p . cp $AMSHOME/examples/adf/green_Al/Au.5p.dirac . $AMSBIN/dirac < Au.5p.dirac mv TAPE12 t12.rel AMS_JOBNAME=Au $AMSBIN/ams <