Talk:Mod:Hunt Research Group/emo

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:

[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA] 
sed -n '252592,504311p' MO_DATA > TM.dat

For example, we want to plot the EMO of Cl#35 from 10 ps:

• Find out which wannier functions belong to the molecule. (2 approaches)
  • [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)

type
sed -n '6874,7741p' LOG_DATA > WAN_MOL

• • Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
• Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].

In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.

• Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
• Use cpmd2cube.x to generate the Wannier cube files.
• Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
• Type: './a.out' to generate the EMO cube files.