Solution LAB2 guanine 4

• Back to the previous page: Electronic properties of isolated molecules#Exercise 4

An example of input file for pp.x to plot the HOMO of guanine (pp_HOMO.in) follows:

&INPUTPP
   prefix="guanine_DFT"
   outdir="./SCRATCH"
   plot_num=7
   filplot = "wfc_HOMO.pp"
   kband=28
   kpoint=1
   lsign=.true.
/
&PLOT
   nfile=1
   filepp(1)="wfc_HOMO.pp"
   iflag=3
   output_format=5
   fileout="wfc_HOMO.xsf"
/

by running as

 pp.x < pp_HOMO.in > pp_HOMO.out

should produce as output the file wfc_HOMO.xsf that can be plotted using xcrysden.

Here is a sketch of the guanine HOMO isosurface:

• Total and projected density of states are calculated using projwfc.x. An example of input file is:

&PROJWFC
 prefix='guanine_DFT'
 outdir="./SCRATCH"
 ngauss=0
 degauss=0.01
/

by running as

projwfc.x < pdos.in > pdos.out 

it produces a file containing the total density of states (guanine_DFT.pdos_tot) and a series of files containing the density of states projected on each atom and each atomic orbital e.g.

guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom

guanine_DFT.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom

The projected dos can be further processed. To obtain the projected dos on a species we can sum up the DOS on all the atoms of the same species using the sumpdos.x executable e.g.:

sumpdos.x guanine_DFT.pdos_*C*  > C.dat
sumpdos.x guanine_DFT.pdos_*N*  > N.dat
sumpdos.x guanine_DFT.pdos_*O*  > O.dat
sumpdos.x guanine_DFT.pdos_*H*  > H.dat