Nanosurf Lab

Once we have obtained an optimized atomic configuration,we can perform electronic structure analysis. To obtain the detail information about energy spectra of the molecule, we perform one-time step run with fixed charges (our optimized structure is stored in ' answer.bas' file). Our fireball.in file looks like:

&OPTION
basisfile = answer.bas
nstepf = 1
icluster = 1
iqout = 1
ifixcharge = 1
dt = 0.5
&END
&OUTPUT
iwrteigen = 1
&END

Finishing the calculation, eigen.dat file appears in the working directory, which lists in ascending order all eigenvalues of molecular orbitals:

         1         142
 --- the energy eigenvalues ---
    -20.77644    -20.17576    -19.32420    -18.49408
   -18.49262    -17.56440    -17.48782    -16.37893
   -16.35960    -14.45772    -13.77290    -12.91450
   -12.55894    -12.31129    -11.72733    -10.57604
   -10.47081    -10.27380     -9.84700     -9.75059
    -9.28453     -9.25281     -8.86563     -8.08602
    -7.86517     -7.84647     -7.63290     -7.56571
    -7.38417     -7.07353     -6.59935     -5.95037
    -5.93908     -5.79952     -4.77435     -3.52791
    -1.31315     -0.15600      0.13238      0.36040
     0.95653      0.98146      1.60240      2.20926
     2.36855      2.46027      2.81924      3.35559
     4.89158      5.47431      5.80665      5.83704
     6.03328      6.93077      6.98308      7.45317
     7.80996      9.21705      9.23329      9.72755
    10.35864     10.52539     11.11532     11.31138
    11.34314     11.65157     11.71850     11.98661
    12.43798     12.47948     12.64843     13.13170
    14.04051     14.19757     14.55861     15.06387
    15.21110     15.30968     15.37279     15.99312
    16.04862     16.43805     16.46738     16.88387
    16.99408     17.25263     17.61341     18.59642
    18.93562     19.46990     19.80628     20.31527
    20.34526     21.40842     21.74713     22.24177
    22.61195     22.76252     23.34774     24.49545
    24.59028     24.93521     25.67988     25.78261
    26.51534     27.32112     27.55584     28.04580
    28.47919     28.76664     29.50683     30.65046
    30.90050     31.21945     33.09324     34.44970
    35.52433     35.86108     37.34994     37.88428
    38.35645     41.40826     42.20641     43.29368
    43.70757     47.36562     48.51939     50.04231
    56.31003     56.38914     60.36281     66.30143
    66.39706     73.75972     87.06108     87.07247
    89.24974     91.64514     93.81909     95.64658
    95.97695     99.09614

In addition, an occupancy of individual molecular level can be written into output file, if keyword ' iwrtefermi' is switched on. In this way energy levels of HOMO and LUMO orbitals can be identified. In our particular case we found in output file:

...
Band n =   24 k-points: ioccupy =  1
Band n =   25 k-points: ioccupy =  1
Band n =   26 k-points: ioccupy =  1
Band n =   27 k-points: ioccupy =  1
Band n =   28 k-points: ioccupy =  1
Band n =   29 k-points: ioccupy =  1
Band n =   30 k-points: ioccupy =  1
Band n =   31 k-points: ioccupy =  1
Band n =   32 k-points: ioccupy =  1
Band n =   33 k-points: ioccupy =  1
Band n =   34 k-points: ioccupy =  1
Band n =   35 k-points: ioccupy =  1
Band n =   36 k-points: ioccupy =  1
Band n =   37 k-points: ioccupy =  0
Band n =   38 k-points: ioccupy =  0
Band n =   39 k-points: ioccupy =  0
Band n =   40 k-points: ioccupy =  0
Band n =   41 k-points: ioccupy =  0
Band n =   42 k-points: ioccupy =  0
Band n =   43 k-points: ioccupy =  0
...

It means last occupied level (HOMO) is no. 36 and first unoccupied level is no. 37. Their eigenvalues can be found in 'eigen.dat' file accounting appropriate number of levels (in ascending order).

Another way how to analyze energy spectra of molecule in Fireball is to calculate Density Of State (DOS). In addition, projected DOS on each atom is provided. To run this task for particular atomic configuration, two steps are necessary:</br> (i) switch on 'iwrtdos' keyword in section '&OUTPUT', so 'fireball.in' looks like now:

&OPTION
basisfile = answer.bas
nstepf = 1
icluster = 1
iqout = 1
ifixcharge = 1
dt = 0.5
&END
&OUTPUT
iwrtdos = 1
&END

(ii) an extra new file called 'dos.optional' has to be created in the working directory with following syntax:

1.0                   ! scale factor (leave 1.0)
1       22            ! list of atoms to analyze DOS
441                   ! number of energy steps
-22.0   0.05          ! initial energy, energy step 
0                     ! leave untouched
0.0     0.0           ! leave untouched
0.05                  ! imaginary part of Green function (controls energy level smearing)

In this particular case, all 22 atoms will be involved in the DOS analysis and DOS will be calculated from energy -22.0 until 0.0 eV with energy step 0.05 eV.

DOS.png

Real-space electronic density

Sometimes is more illustrative visualize electron density in real-space. This can help can be of use as primitive estimation of STM images or it can provide more information about spacial (de)localization certain molecular levels. Here we'll visualize HOMO and LUMO state of the molecule. To do this, we need to first switch on keyword 'iwrtewf' in 'fireball.in' file (the section '&OUTPUT'). As a next step, we need to create a new section in 'fireball.in' called '&MESH' with following keywords:

&MESH
iewform = 1               ! individual levels listed bellow will be plotted in separated files 
npbands = 2               ! number of molecular levels to be plotted
pbands =36,37             ! list of molecular levels to be plotted 
&END

Real-space densities of individual molecular levels are stored in bandplot_XXXX.xsf files, where XXXX means number of given molecular orbital. These files are stored in an internal format of visualization program [http://www.xcrysden.org XCrysden].

real density of state of the HOMO molecular state