Talk:Mod:Hunt Research Group/emoplot

How to use my emo plot code. At the moment the code is system dependent, so need to modify the code depending on the system.

Use gfortran on imac to compile the following codes.

[wc2emo1.f90 https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:Wc2emo2.f90] for EMO1-4 (Note: use Wannier functions 1 4 6 7)

[wc2emo2.f90 https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:Wc2emo2.f90] for EMO5-8 (Note: use Wannier functions 2 3 5 8)

Note: don't forget to change Wfindex.dat!

e.g. for a water dimer i7, i8, i9, i10, i11, i12 representing the six atoms (8, 8, 1, 1, 1, 1) in the system.

e.g. for a Cl- + H2O i7, i8, i9, i10 representing the four atoms (17, 8, 1, 1) in the system.

When visualising using VMD, copy the header of the WANNIER_1.1.cube to EMO1.cube, etc.

1. Example on gas-phase system: a water dimer. water molecule 1 = solute. water molecule 2 = solvent.

Input files:

(a) Wfindex.dat

Get the indices from WAN_CENT from the EMO analysis. e.g. part of the WAN_CENT file is as below:

mol.unit_atom_wannier

  1    1    1
  1    1    4
  1    4    6
  1    3    7
  2    6    2
  2    2    3
  2    2    5
  2    2    8

So the Wfindex.dat file looks like this:

(b) TM.dat

Get the transformation matrix using the section MO_vectors_in_wannier_basis from MO_DATA from the EMO analysis. e.g.

MO_vectors_in_wannier_basis

 0.380745330483581      -0.387048685730658      -0.593829545672107
 0.593795233119951       0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000  0.000000000000000E+000
 3.818204221663405E-005  6.597957813054027E-006  0.707096441679227
 0.707117119481048       0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000  0.000000000000000E+000
 0.555754552974222      -0.630061645514137       0.383503124705457
-0.383516040135992       0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000  0.000000000000000E+000
 0.739033063337157       0.673212921506009       1.750560460493717E-002
-1.755127970424728E-002  0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000 -0.597255009304460       0.589852831249687
 0.384260755449986      -0.384322472864214
 0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000 -0.710690459177621      -0.703281622962521
-1.253377524729020E-002  1.252735068381089E-002
 0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000 -0.371760035109413       0.396823126740195
-0.593306535305625       0.593559801151676
 0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E+000
 0.000000000000000E+000 -3.728376770054018E-005  4.851872010664688E-005
-0.707229758609386      -0.706983779724233

And the file TM.dat would look exactly the same as above section. If wc2emo1.exe has trouble reading this file, open TM.dat using vi, then do

set ff=unix

and then save it with :wq.

(c) WANNIER_1.X.cube files X=1,2,3,4,5,6,7,8

(d) Depending on which EMO to plot, need to change the number in the code

EMOindex = ? (? = 1, 2, ... or 8)

open(unit=100, file='EMO?.cube', status='new') (? = 1, 2, ... or 8)

4. The Plots