How the separate each fragment alone of an IRC task ?

maximos

Hi,
I'm computational chemistry PhD student, and this is my first time on the forum. I would like to ask a question about the fragment analysis of a reaction.
Accordig to my researchs i found some tools like Excelautomat 1.3, PyFrag2019 to perform the fragment analysis automatically, but it didn't work for me, and i decided to make the whole work manually.
My question is, how could i separate each fragment alone of an IRC calculation, for example I performed an IRC task of Diels- Alder reaction, and i want to separate the ethylene and butadiene along the IRC.
Note: the program used is Gaussian 09 D.01

My thanks in advance
Maximos


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北大-陶豫

Do you mean you want to separate C2H4 and C4H6 in every structure of the IRC task?
These two points might be helpful:
(1) In a structure every atom has a number (1, 2, ..., N, N is the number of atoms) which does not change diring the whole IRC job. You can just follow the number to know which is the fragment of interest.
(2) Gaussian calculates the density matrix once a structure is given, and the distances are given in the output file (.log or .out). You can write a script (also GView can do this automatically I guess) to judge the bonding situations and then judge which atoms are connected as a part(fragment) while others are not.

maximos

Dear colleague,
You got me right, that's what i'm looking for, but the problem i don't know how to start. Could you help me, please ?

北大-陶豫

maximos 发表于 2021-2-1 14:43
Dear colleague,
You got me right, that's what i'm looking for, but the problem i don't know how to  ...

Load your file into GView and then tick View->Labels:


The labels of atoms are consistent with their sequences in your input file.
In the case above, if you want to follow the C2H4 fragment you just follow the atoms No. 4 5 11 12 13 14 in each structure of the IRC job.

maximos

Thank you very much for your effort, and about the separation process, How can i do it ? It must be done automatically.

北大-陶豫

maximos 发表于 2021-2-1 15:03
Thank you very much for your effort, and about the separation process, How can i do it ? It must be  ...

In your output file (.log or .out) you can search "Input orientation", which is followed by the cartesians of the atoms. Based on this you can design your script.

北大-陶豫

maximos 发表于 2021-2-1 15:03
Thank you very much for your effort, and about the separation process, How can i do it ? It must be  ...

I have written a script before, which monitors the optimization process of a Gaussian job.
See Converge_Reader.cpp in https://github.com/Tao-Yu-Chem/GaussianScripts/

You can change its code to meet your requirements.

maximos

Dear Colleague,
Thank you very much for your time and help, i truly appreciate it.
The link that provide is not working. (Not found)

冰释之川

How to convert outputs of IRC jobs to the *.xyz trajectory files:
http://sobereva.com/285（http://bbs.keinsci.com/thread-850-1-1.html）

Convert *.xyz trajectory file to the  separated *.xyz files:
Multiple_XYZ_Split.py (2.13 KB, 下载次数 Times of downloads: 4)

2021-2-1 17:29 上传 Uploaded

点击下载
Click to download

If you have obtained the separated *.xyz files from IRC jobs, you can use this python script to extract coordinates of each fragment
XYZ_Coordinate_Extraction.py (4.51 KB, 下载次数 Times of downloads: 2)

2021-2-1 15:32 上传 Uploaded

点击下载
Click to download

北大-陶豫

maximos 发表于 2021-2-1 15:31
Dear Colleague,
Thank you very much for your time and help, i truly appreciate it.
The link that  ...

Sorry, I don't know why but just copy the link into your browser

maximos

Dear Colleagues,
Thank you very much for your help, everythings works fine.