Symmetry problem

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ndhieu92
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Symmetry problem

Post by ndhieu92 » 12 Oct 2019, 05:49

Good day everyone.

I am having a question, and please help me to point out which is right. I attached two output file of spin-orbit coupling constant calculation below.
I tried with nosymmetry and automatic symmetry detection in atomic mean-field approximation method (AMFI method). The results of SOCs value are different apparently, however, I can see the warning inside the output, for example, in the output nosymmetry:

--
WARNING: Solution vector on RSPVEC converged to 1.39D-01
WARNING: which is less than desired convergence 1.00D-03

@ WARNING---- Response label Z1MNF-SO with frequency -0.52889160
and symmetry 1 not converged on file RSPVEC

--

Please help me know what this warning means and how it affects my calculation. Should I explicitly specify the symmetry for my molecule or not?

Thank you so much and Best regards.
Attachments
SPINORBIT_rsplrso_AMFI_quadratic_nosymmetry_SOC_ISODOLINE_mol3.out
(319.5 KiB) Downloaded 11 times
SPINORBIT_rsplrso_AMFI_quadratic_autosymmetry_SOC_ISODOLINE_mol3.out
(319.52 KiB) Downloaded 7 times

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magnus
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Re: Symmetry problem

Post by magnus » 12 Oct 2019, 10:10

You're using automatic symmetry detection in both cases because the "Nosymmetry" keyword in your input is placed in one of the comment lines. It has to be in the next line together with the "Atomtypes" keyword etc., i.e.

Code: Select all

Atomtypes=5 Angstrom Nosymmetry
However, in this case it doesn't matter because there is no symmetry so Dalton detect just C1. Not sure if there is supposed to be symmetry but in any case there is something wrong with your molecule input (see attached image) which is most likely why you're seeing warnings and getting weird results.
Screenshot from 2019-10-12 11-04-26.png
(250.83 KiB) Not downloaded yet

ndhieu92
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Re: Symmetry problem

Post by ndhieu92 » 12 Oct 2019, 13:49

magnus wrote:
12 Oct 2019, 10:10
You're using automatic symmetry detection in both cases because the "Nosymmetry" keyword in your input is placed in one of the comment lines. It has to be in the next line together with the "Atomtypes" keyword etc., i.e.

Code: Select all

Atomtypes=5 Angstrom Nosymmetry
However, in this case it doesn't matter because there is no symmetry so Dalton detect just C1. Not sure if there is supposed to be symmetry but in any case there is something wrong with your molecule input (see attached image) which is most likely why you're seeing warnings and getting weird results.
Screenshot from 2019-10-12 11-04-26.png
Thank you so much Dr. Olsen for your suggestion. Actually, I tried to make the molecule input by using the Mol file extracted from the optimized molecule by using Gaussview software, so the order of Carbon, Hydrogen, Fluoride, Boron and Nitrogen was kept as their appearance in the Mol file.

I attached the optimized molecule file and also the MOL.file which I extracted from the optimized molecule by gaussview software. May I ask you which software did you use to rebuild the structure of molecule by using data from MOL.file ?

Thank you so much.
Attachments
ISODOLINEBODIPY3B2.log
(1.4 MiB) Downloaded 7 times
ISODOLINEBODIPY3B2.txt
(4.49 KiB) Downloaded 7 times
ISODOLINEBODIPY3B2.mol
(4.49 KiB) Downloaded 6 times

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magnus
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Re: Symmetry problem

Post by magnus » 12 Oct 2019, 13:55

You should always check the output of your calculations. In your geometry optimization, you asked for vibrational frequencies, which can be used to make sure that you have indeed reached a minimum. In your case, you have one imaginary frequency (search for "imaginary frequencies" in your output from Gaussian). This means that it is not a minimum but rather a transition state.

I manually converted the mol file to xyz and used avogadro to view it.

ndhieu92
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Re: Symmetry problem

Post by ndhieu92 » 12 Oct 2019, 15:27

magnus wrote:
12 Oct 2019, 13:55
You should always check the output of your calculations. In your geometry optimization, you asked for vibrational frequencies, which can be used to make sure that you have indeed reached a minimum. In your case, you have one imaginary frequency (search for "imaginary frequencies" in your output from Gaussian). This means that it is not a minimum but rather a transition state.

I manually converted the mol file to xyz and used avogadro to view it.
Thank you so much Dr. Olsen.

I will be careful about that problem. I am trying to optimize again and make sure it is global minimum structure instead of TS and remake the input file

hjaaj
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Re: Symmetry problem

Post by hjaaj » 14 Oct 2019, 10:02

Your output shows that there are lot of complex eigenvalues both in the calculation of the singlet excitation vector+energy and of the triplet one. This means that your reference state calculation is not OK and therefore you cannot trust any of the results. I think the DIIS converged to a stationary state instead of the minimum. You could try doing a Hartree-Fock first and start B3LYP from the converged Hartree-Fock orbitals. No guarantee for success.

ndhieu92
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Re: Symmetry problem

Post by ndhieu92 » 15 Oct 2019, 02:10

hjaaj wrote:
14 Oct 2019, 10:02
Your output shows that there are lot of complex eigenvalues both in the calculation of the singlet excitation vector+energy and of the triplet one. This means that your reference state calculation is not OK and therefore you cannot trust any of the results. I think the DIIS converged to a stationary state instead of the minimum. You could try doing a Hartree-Fock first and start B3LYP from the converged Hartree-Fock orbitals. No guarantee for success.
Thank you so much for your comments, Dr. Hans Jorgen. I tried to optimize again and calculate them again

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