Multiwfn forum

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

transition density matrix

Hi there

How do you create an output file that contains three lines that represents fragments within a molecule?

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

Dear Louis-Charl,

Could you please describe your question in more detail? I don't know what does "three lines" mean.

Best regards,

Tian

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

On page 647 in the previous version of the manual, they describe a method for the transition density matrix between 5 fragments, but requires  a txt file with the 5 rows which represent each fragment. According to the manual, the numbers correspond to the codes used for each atom. How do you produce this txt file?

Thanks inb advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

Do you mean this file?

If yes, you should manually create this file using a text editor. From main function 0 or any other visualization software, you can identify the indices of atoms in each fragment.

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

I have managed to manually create the tdm.txt file in notepad and also created the fchk file for the TDM. However, it still gives me error messages.

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

It is best to send me your input files for Multiwfn and the tdm.txt you created to my E-mail, and also show me all commands you inputted in Multiwfn, I will check.

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

I've e-mail you the requested files thanks

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

I have received your files, but you didn't provide me a file containing definition of the fragments.

After selecting option "-1 Define fragments" in the TDM plotting interface, as described in "Fragment transition density matrix" part of Section 4.18.2.2 of manual, you should either directly input the indices of the atoms in each fragment, or provide a file containing indices of the atoms in every fragment. If you prefer the latter, the provided file should contains several lines, each line contains indices of the atoms in the fragment, such as
1-23
24-33
34-43
Then three fragments will be loaded, they correspond to atoms 1-23, 24-33 and 34-43, respectively. Then you can choose option "1 Show transition matrix map" to plot TDM between the three fragments.

You have sent me a plain text file tdmat.txt, which, however, is completely irrelevant to the current situation.

If you are still confused, please follow the following steps for example

Create a file "fragdef.txt" with following content, we define three fragments
58-67,88-107,109
48-57,68-87,108
1-46

Then boot up Multiwfn and input
Oxadiaz-starburst-TD-DFT-M06.fchk
18
2  // Plot TDM map
Oxadiaz-starburst-TD-DFT-M06.log
2  // Study the second excited state
n
1
-1  // Define fragment
0  // Load fragment definition from a plain text file
fragdef.txt
1  // Plot

Now you will see TDM map between the three fragments.

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

Thank you for your response. However, I still do not know how to create fragmentdef.txt file. Can you please assist me with this?

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

Just open notepad or other text editor, input the following three lines, then save as fragdef.txt.
58-67,88-107,109
48-57,68-87,108
1-46

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

Hi there

When I plot absorption and emission spectra for some of my compounds then there are not big shifts in wavelengths. For some compounds there are very tiny shifts. Does this have anything to do with the imaginary frequencies of the compounds. If it does, how can I rectify them?

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

Hi there

When I plot absorption and emission spectra for some of my compounds then there are not big shifts in wavelengths. For some compounds there are very tiny shifts. Does this have anything to do with the imaginary frequencies of the compounds. If it does, how can I rectify them?

Thanks in advance

Regards
Louis-Charl

I don't understand your problem and your representation. Absorption and emission spectra are electronic spectra, they are completely irrelevant to imaginary frequencies.

Louischarlc0

Member

Registered: 2020-07-21

Posts: 63

Re: transition density matrix

But why do they state in the multiwfn manual on page 568 that they were testing the log file for imaginary frequencies before performing the analysis for the fluorescence spectrum?

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: transition density matrix

Fluorescence emission occurs at minimum of potential energy surface of S1 state (assume that Kasha's rule works in this system), therefore, in order to confirm that the current structure is indeed a minimum, frequency analysis should be conducted for S1 state to ensure that there is no imaginary frequency at current structure.