help

mest2309 · 2018-03-26 15:48:48

Dear all,

Hope we are ding fine , I am a PHD student who works with a team in Grenoble France who developes organic materials for photovoltaic applications, recently we developed four organic materials and to evaluate our work we did a theoretical study to confirm the experience !! since I do not understand how to do the simulations, I ask theoretical friends to simulate for me the optical spectrum and orbitals moleculars ! I received a reversion from review of the journal to plot Electron Density Difference and not orbitals moleculars to show the charge transfer and he told me to do it with Multiwfn and cite it in Computational details section !! so I did a search on this software and I join this forum and I find much helpful peopel here !! can we help me to draw the Electron Density Difference S0→S1 for me to revise my paper and will accept !! If I find one I will join the input and output files and hope that I receive an answer that's makes me happy .

Best regards,

I_was_a_baby · 2018-03-27 01:18:23

mest2309 wrote:

Dear all,
Hope we are ding fine , I am a PHD student who works with a team in Grenoble France who developes organic materials for photovoltaic applications, recently we developed four organic materials and to evaluate our work we did a theoretical study to confirm the experience !! since I do not understand how to do the simulations, I ask theoretical friends to simulate for me the optical spectrum and orbitals moleculars ! I received a reversion from review of the journal to plot Electron Density Difference and not orbitals moleculars to show the charge transfer and he told me to do it with Multiwfn and cite it in Computational details section !! so I did a search on this software and I join this forum and I find much helpful peopel here !! can we help me to draw the Electron Density Difference S0→S1 for me to revise my paper and will accept !! If I find one I will join the input and output files and hope that I receive an answer that's makes me happy .
Best regards,

Dear my friend,

The method how to plot the Electron Density Difference between S0 and S1 must be what I tell you, I believe, if I haven't misunderstood.

First things first, you have to take two computational jobs by Gaussian to obtain the wave function file of S0 and S1. So, the key word of input files of S0 and S1 are following respectively:

"# [DFT]/[basis set] TD(nstate=N)" for S0
"# [DFT]/[basis set] TD(nstate=N) density" for S1

where N is the number of excited states. And "root=1" in this situation is acquiescent, so it isn't applied. Please Keep in mind that the name of two .chk files must be different.

After computations, using formchk module of Gaussian to transform the .chk files to .fch files, then we can use the Multiwfn program.
Please start Multiwfn program, and the S0.fch should be loaded.

S0.fch
5
0
1
-,S1.fch
1
-10 // this option is used to change the extansion distance. If you don't want to change in there, Please modify the value of "aug3D" in setting.ini
10 //10 Bohr
2
-1 //preview isosurface

Then you can save the picture. If you want to improve character of your plot, the VMD program should be used.
More details can be found in 4.4.5 of Multiwfn manual.

Best wishes
wawa
2018-03-27

mest2309 · 2018-03-27 10:39:11

Dear frend ,
thanks for reply, I can not describe how your answer let's me happy ! I did all the imput file as you proposed to me but have this problem

best regards,
Mest

I_was_a_baby · 2018-03-27 10:56:05

mest2309 wrote:

Dear frend ,
thanks for reply, I can not describe how your answer let's me happy ! I did all the imput file as you proposed to me but have this problem

https://s9.postimg.org/6msxrfzx7/help.png
best regards,
Mest

Friend:

In this situation, the order of "formchk" haven't been defined in environment variables.

There are two ways to solve this problem:
1, the order of "formchk" should be defined in environment variables.
2, finding the route of formchk module, then using absolute path to transform the .chk file.

For example, after open output files of Gaussian, you can be find this:

Then absolute path of formchk module is "/opt/soft/Gauss/Gauss09.E01/g09/formchk".

So you can transform your .chk files and finish the following jobs.

wawa
2018-03-27

mest2309 · 2018-03-27 11:21:07

Dear frend ,

Think you a lot WAWA , you are a very helpful person , I dont understand what you say because I am not a theoretical person !! So I can't find a solution for this problem !! hope the best and success for you

Mest

I_was_a_baby · 2018-03-27 11:56:12

mest2309 wrote:

Dear frend ,
Think you a lot WAWA , you are a very helpful person , I dont understand what you say because I am not a theoretical person !! So I can't find a solution for this problem !! hope the best and success for you
Mest

According to the way what I tell you above, when you write the following order on command line of Linux system:

/opt/soft/Gauss/Gauss09.E01/g09/formchk S0.chk
[Enter]

then you can transform the .chk file to .fch file, where the route of "/opt/soft/Gauss/Gauss09.E01/g09/formchk" can be changed according to your own situation.

If you fail to understand my answer how to transformthe .chk file to .fch file, please read the Gaussian manual carefully.

wawa

sobereva · 2018-03-28 14:27:06

Dear mest2309,

The way of generating density difference map between excited state and ground state in fact has been substantially illustrated in Section 4.18.3 of the manual.

The easiest way to do this is generating .wfn file for S0 and S1, respectively, and then use custom operation of main function 5 to plot the isosurface map.

First, optimize your molecule at S0 state to generate the S0 geometry, and then use below input file to generate .wfn file for S0:

# B3LYP/6-311G** out=wfn
test
0 1
[Optimized S0 geometry]
C:\S0.wfn

Then use this file to generate .wfn for S1

# B3LYP/6-311G** TD density out=wfn
test
0 1
[Optimized S0 geometry]
C:\S1.wfn

Next, boot up Multiwfn and input following commands
C:\S1.wfn // Load excited state wavefunction file
5 // Generate grid data
0 // Set custom operation
1
-,C:\S0.wfn // Property of ground state wavefunction will be substracted from that of excited state wavefunction
1 // The property to be studied is electron density
2 // Medium quality grid (if your system is large, select 3 to use high quality grid to get better result)
-1 // Visualize isosurface

Then you will see density difference isosurface map corresponding to rho(S1)-rho(S0) at S0 geometry, the map exhibits the charge redistribution during vertical excitation. You can adjust "isovalue" parameter in the GUI window to make the graph looks better.

Best regards,

Tian

sobereva · 2018-03-28 14:30:40

I_was_a_baby,

I don't suggest using .fch file to plot the S0-S1 difference map, because you have to convert the density matrix of excited state to corresponding natural orbitals (Multiwfn only loads orbitals from .fch file rather than density matrix), this requires an additional step. Clearly, using .wfn or .wfx file is more convenient.

Tian

mest2309 · 2018-03-28 19:02:27

Tian

how to transform .chk file to .wfn or .wfx file

Mest

sobereva · 2018-03-29 02:30:50

mest2309 wrote:

Tian
how to transform .chk file to .wfn or .wfx file
Mest

You don't need to transform it, just redo the calculation with out=wfn keyword, the .wfn/.wfx file will be generated to your specified path. Please check beginning of Chapter 4 of Multiwfn manual for details and examples of generating .wfn/.wfx files.

PS: In fact, you can directly use .fch of ground state instead of .wfn of ground state. However, .fch of excited state cannot be directly used, because by default the orbitals stored in this file correspond to ground state orbitals.

krjt · 2023-11-02 16:40:09

This is a fairly good tutorial for density difference map between excited state and ground state from the outputs of Gaussian calculations.

How to generate wfn files required for this task from ORCA calculations?

Your help will be much appreciated.

krjt

sobereva wrote:

Dear mest2309,
The way of generating density difference map between excited state and ground state in fact has been substantially illustrated in Section 4.18.3 of the manual.
The easiest way to do this is generating .wfn file for S0 and S1, respectively, and then use custom operation of main function 5 to plot the isosurface map.
First, optimize your molecule at S0 state to generate the S0 geometry, and then use below input file to generate .wfn file for S0:
# B3LYP/6-311G** out=wfn
test
0 1
[Optimized S0 geometry]
C:\S0.wfn
Then use this file to generate .wfn for S1
# B3LYP/6-311G** TD density out=wfn
test
0 1
[Optimized S0 geometry]
C:\S1.wfn
Next, boot up Multiwfn and input following commands
C:\S1.wfn // Load excited state wavefunction file
5 // Generate grid data
0 // Set custom operation
1
-,C:\S0.wfn // Property of ground state wavefunction will be substracted from that of excited state wavefunction
1 // The property to be studied is electron density
2 // Medium quality grid (if your system is large, select 3 to use high quality grid to get better result)
-1 // Visualize isosurface
Then you will see density difference isosurface map corresponding to rho(S1)-rho(S0) at S0 geometry, the map exhibits the charge redistribution during vertical excitation. You can adjust "isovalue" parameter in the GUI window to make the graph looks better.
Best regards,
Tian

sobereva · 2023-11-02 22:24:25

krjt wrote:

This is a fairly good tutorial for density difference map between excited state and ground state from the outputs of Gaussian calculations.
How to generate wfn files required for this task from ORCA calculations?
Your help will be much appreciated.
krjt

Please check http://sobereva.com/wfnbbs/viewtopic.php?id=306

krjt · 2023-11-03 09:46:19

Thank you very much.

Sorry to bother you.

How to get the molden.input file for ground state? Is it from ground state optimization file, ex., opt.gbw?

krjt

sobereva · 2023-11-04 08:13:49

krjt wrote:

Thank you very much.
Sorry to bother you.
How to get the molden.input file for ground state? Is it from ground state optimization file, ex., opt.gbw?
krjt

You just need to perform a ground state calculation, then a .gbw file will yield, and then you can use orca_2mkl to convert it to .molden.input file containing ground state wavefunction.

krjt · 2023-11-06 05:23:54

Thanks for confirming my query.

krjt

Multiwfn forum

#1 2018-03-26 15:48:48

help

#2 2018-03-27 01:18:23

Re: help

#3 2018-03-27 10:39:11

Re: help

#4 2018-03-27 10:56:05

Re: help

#5 2018-03-27 11:21:07

Re: help

#6 2018-03-27 11:56:12

Re: help

#7 2018-03-28 14:27:06

Re: help

#8 2018-03-28 14:30:40

Re: help

#9 2018-03-28 19:02:27

Re: help

#10 2018-03-29 02:30:50

Re: help

#11 2023-11-02 16:40:09

Re: help

#12 2023-11-02 22:24:25

Re: help

#13 2023-11-03 09:46:19

Re: help

#14 2023-11-04 08:13:49

Re: help

#15 2023-11-06 05:23:54

Re: help

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