Nanosurf Lab

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====== Scissor operator ======
 (by Enrique)

Scisor operator computation is composed from 3 steps
    - Export molecular orbitals coefficients from free standing molecule SCF by setting  iwrtcdcoefs = 1
    - set koopmans shifts for orbitals of molecule (file koopman_shift)
    - run SCF of molecule on electrodes with gap correction on (igap = 3)

===== Free molecule computation =====

As example you can use fireball.in like this ( importaint is to se iwrtcdcoefs = 1 )

<code>
&OPTION
basisfile = freemol.bas 
lvsfile = cel.lvs
icluster = 0
nstepf = 1
sigmatol = 0.000001
max_scf_iterations = 100
iqout = 0
ifixcharge = 0
&END

&OUTPUT
iwrtcdcoefs = 1
&END
</code>

<code>
12
   8     -0.000000      0.006964     -0.307366
   6      0.000000     -0.001848      1.561491
   1      0.000000     -2.253742      1.713401
   1      0.000000      2.250737      1.711678
   6      0.000000     -1.242741      2.296730
   6      0.000000      1.240398      2.295749
   6     -0.000000     -1.240740      3.721606
   6     -0.000000      1.239884      3.720292
   1     -0.000000     -2.253492      4.301542
   1     -0.000001      2.253787      4.299402
   6     -0.000000      0.000210      4.460464
   8      0.000000      0.000069      6.330528
</code>

===== SYSTEM computation =====

   - copy cdcoeffs.dat from molecule computation to the SYSTEM directory
   - Set koopmans shifts for orbitals of molecule. To do this you should specify start and end atom of molecule inside the system geometry file. Ten set number of molecular orbitals (the same number as first number of molecular cdcoefs.da) to be shifted and specify shifts for each of the orbitals.

koopman_shift
<code>
19        first_atom
30        last_atom
76        orbitals
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
  -1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
   1.00000
</code>

then you can run computation with (igap=3), see this fireball.in as a reference

fireball.in
<code>
&OPTION
basisfile = answer_small.bas 
lvsfile = cel.lvs
icluster = 0
nstepf = 1
sigmatol = 0.000001
max_scf_iterations = 100
dt = 0.5
iqout = 0
ismeagol=0
ifixcharge = 0
igap = 3
&END

&OUTPUT
iwrtHSrho = 0
iwrteigen = 0
iwrtdos = 0
&END
</code>
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