I have several conformers for which I wanted to plot the averaged weighted spectra. The number of atoms are same. However, the atom numberings are different. As a result, the spectra I am getting is incorrect. Is there any quick way to resolve this issue ? or can I use a bash script where I process multiple output files and generate the spectra of all the conformers and then average the spectra.

Thanks,
Sibali

Dear Marcin Andrzejak,

I am sorry that I am not a Turbomole user, I don't know what is .cao file...

Best,

Tian

The dipole moment obtained by Multiwfn in this way corresponds to unrelaxed excited density, while directly using "density" keyword will make Gaussian output dipole moment corresponding to relaxed excited density at final part of the output file. If you use "density=rhoci" instead, the dipole moment given by Gaussian will also correspond to unrelaxed excited density.

See example:

#p b3lyp/6-31G* iop(9/40=4) density=rhoci TD(root=2) b3lyp/6-311G* opted 0 1 C 0.00000000 1.09275900 0.34582000 C 0.00000000 0.71582300 -0.95557500 C 0.00000000 -0.71582300 -0.95557500 C 0.00000000 -1.09275900 0.34582000 O 0.00000000 0.00000000 1.15706000 H 0.00000000 2.04717300 0.84155100 H 0.00000000 1.36964900 -1.81125900 H 0.00000000 -1.36964900 -1.81125900 H 0.00000000 -2.04717300 0.84155100

Finally Gaussian outputs

 Dipole moment (field-independent basis, Debye): X= 0.0000 Y= 0.0000 Z= -1.0345 Tot= 1.0345

Multiwfn outputs

 Transition electric dipole moment between excited states (a.u.): i j X Y Z Diff.(eV) Oscil.str 1 1 0.0000000 -0.0000000 -0.5354110 0.00000 0.00000 1 2 -0.0000000 -1.6938922 -0.0000000 0.43340 0.03047 1 3 -0.0308571 -0.0000000 0.0000000 1.57400 0.00004 2 2 0.0000000 -0.0000000 -0.4084153 0.00000 0.00000 2 3 0.0000000 -0.0000000 -0.0000000 1.14060 0.00000 3 3 0.0000000 0.0000000 1.2196069 0.00000 0.00000

Pay attention to the Z component of the 2nd excited state given by Multiwfn, -0.4084153 a.u. *2.5417462 = -1.038 Debye, which is in good agreement with the -1.0345 printed by Gaussian.

However, if you use "density" rather than "density=rhoci", Gaussian prints

 Dipole moment (field-independent basis, Debye): X= 0.0000 Y= 0.0000 Z= -0.8180 Tot= 0.8180

The result is not so close to Multiwfn.

By the way, when "nosymm" is not used, Gaussian automatically translates the system so that the origin is at center of nuclear charges, in this case contribution of nuclei to dipole moment is exactly zero, and thus you do not need to check the contribution.

Best regards,

Tian

Dear Prof. Tian,

Thanks a lot.

Thank you very much.
Saeed

Tian,

This is really interesting. I also checked a citation in your paper wherein many molecules were screened for their charge separation or local polarity (PI-index) from Tore Brinck, Jane S. Murray & Peter Politzer.
They had CO2 in their dataset and actually got a large value for PI = 16.2 kcal/mol (my value from a very different DFT theory is close to 11.2 kcal/mol but close enough). They suspect this is because of high degree of charge separation in the molecule, which cannot be captured from dipole moment, just like you mentioned.

I look into what other descriptors can I extract from Multiwfn to see what correlates best with my experimental data.

Thank you once again

Best regards,
Pranav

The easiest way is: Performing orbital localization first, and then enter main function 0, in the menu select "Other settings" - "Choose plotting wavefunction or density" - "Density". Then if you select an orbital, the orbital probability density will be shown as isosurface map.

If you really want to use third-part software to visualize the orbital probability density, you should:
(1) Performing orbital localization
(2) Enter main function 6, use subfunction 26 to set occupation of all orbitals to 0, and then set occupation of the orbital of interest to 1. Return to main menu
(3) Using main function 5 to calculate grid data of electron density, in this case electron density corresponds to probability density of the orbital. Then export the grid data as .cub file in the post-processing menu.
(4) Use VMD, VESTA, ChimeraX and so on to visualize the isosurface based on the .cub file (I am not a IQmol user, I don't know if it supports .cub file)

In the RESP module of Multiwfn you can set charge constraint(s) using option "6 Set charge constraint in fitting", I think if you constraint the charge of the oxygen to zero, you can realize your aim.

The net charge and spin multiplicity are directly reflected by the wavefunction information recorded in the molden file, so you do not need to explicitly tell Multiwfn these information, you just need to make sure that you have specified correct net charge and spin multiplicity in your ORCA calculation.

I think you didn't correctly configuration the running environment, please check Section 2.1.2 of Multiwfn manual on how to install Multiwfn in a fully correct way.

Thank you for the suggestion! As my text editor, I had been using Xed, which does not have "column mode". Now I have switched to Geany, which does have column mode. It works very well! Thank you again.

You can see the following energy terms are extracted from final.out

E_tot_final=`grep "SCF Done" final.out | awk -F = '{print $2}'| awk '{print $1}'` E_T_final=`grep "ET=" final.out | awk -F = '{print $2}' | awk '{print $1}'` E_x_final=`grep "ENTVJ=" final.out | awk -F = '{print $3}' | awk '{print $1}'` E_c_final=`grep "ENTVJ=" final.out | awk -F = '{print $4}' | awk '{print $1}'` ... E_disp_final=`grep "Dispersion energy" final.out | awk -F = '{print $2}'| awk '{print $1}'` ... E_tot_frz=`grep " E=" final.out | head -1 | awk '{print $2}'`

Before running these and subsequent lines in the sobEDA.sh, you only need to replace the values after "SCF Done", "ET=", "ENTVJ=" in final.out with those in final2.out.

Yes, you are quite right.
Using "density=current" leads both SCF and MP2 densities to be saved in the "chk" file which could simply viewed when "chk" is converted into a readable format such as "fch". But, if such "chk" file is directly loaded into Multiwfn, only SCF density is taken into account for AIM analysis. Consequently, to avoid an additional calculation (out=wfn, density=current leading to wavefunction file with MP2 density, the procedure) recommended by Tian is the best and perfect.

Saeed

Dear Tian,
Many many thanks for your highly valuable, professional, and novel comments. I was so enjoyed and learned.

Sincerely,
Saeed

Thank you very much for your response.