Calculation of spin orbit coupling constant

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ndhieu92
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Calculation of spin orbit coupling constant

Post by ndhieu92 » 05 Sep 2019, 15:49

Hi everyone,

I am a very newbie to DALTON, so right now I am having a project which is related to calculate the spin-orbit coupling constants Hso between First Lowest Singlet and Triplet Excited States, calculated at B3LYP/6-31G-(d)//M06. My molecule is BODIPY, you can check it at this paper: " Theoretical Determination of Electronic Spectra and Intersystem Spin−Orbit Coupling: The Case of Isoindole-BODIPY Dyes" (dx.doi.org/10.1021/ct500426h | J. Chem. Theory Comput. XXXX, XXX, XXX−XXX)

Can you help me to edit input file?

Thank you so much :oops:
Attachments
SPINORBIT_rsplrso_SOC_ISODOLINE.out
(105.59 KiB) Downloaded 16 times
SPINORBIT_rsplrso.dal
(901 Bytes) Downloaded 19 times
SOC_ISODOLINE.mol
(2.22 KiB) Downloaded 15 times
Last edited by ndhieu92 on 28 Sep 2019, 05:48, edited 2 times in total.

hjaaj
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Re: Calculation of spin orbit coupling constant

Post by hjaaj » 06 Sep 2019, 10:23

I suggest that you e-mail the authors of that paper and ask them to send you a copy of the relevant dalton input files.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 06 Sep 2019, 12:13

thank hjaaj for your comment, haha. That is a very good idea.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 26 Sep 2019, 11:56

hjaaj wrote:
06 Sep 2019, 10:23
I suggest that you e-mail the authors of that paper and ask them to send you a copy of the relevant dalton input files.
hjaaj, Could you take a look on my file and let me know what is wrong with my input file so the calculation stops. Thanks

hjaaj
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Re: Calculation of spin orbit coupling constant

Post by hjaaj » 26 Sep 2019, 12:19

You have to look at the log file, there is no error message in the output file. One guess is that your disk ran full, the 2-electron spin-orbit integrals will use a lot of disk space.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 27 Sep 2019, 01:56

hjaaj wrote:
26 Sep 2019, 12:19
You have to look at the log file, there is no error message in the output file. One guess is that your disk ran full, the 2-electron spin-orbit integrals will use a lot of disk space.
Thanks a lot, I will try again

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Re: Calculation of spin orbit coupling constant

Post by xiongyan21 » 28 Sep 2019, 04:56

I have tried it using Dalton2016.2, and found the output is slightly different
...
The following one-electron property integrals are calculated as requested:
- overlap integrals
- spatial spin-orbit integrals

Center of mass (bohr): 0.000000000000 0.000000000000 0.001198145780
Operator center (bohr): 0.000000000000 0.000000000000 0.000000000000
Gauge origin (bohr): 0.000000000000 0.000000000000 0.000000000000
Dipole origin (bohr): 0.000000000000 0.000000000000 0.000000000000


************************************************************************
************************** Output from HERINT **************************
************************************************************************

Time used in ONEDRV is 1.21 seconds
Time used in HUCKEL is 0.49 seconds
Time used in OVERLAP is 0.14 seconds
Time used in POPOVLP is 0.29 seconds
Time used in DIPLEN is 0.17 seconds
Time used in QUADRUP is 0.33 seconds
Time used in KINENE is 0.27 seconds
Time used in SPNORB is 1.54 seconds
Time used in GABGEN is 1.11 seconds
Total CPU time used in HERMIT: 5.55 seconds
Total wall time used in HERMIT: 5.66 seconds
...,
but it seems the calculation can move on although it may me time-consuming
...

***********************************************
***** DIIS acceleration of SCF iterations *****
***********************************************

C1-DIIS algorithm; max error vectors = 8

Automatic occupation of symmetries with 316 electrons.

Iter Total energy Error norm Delta(E) SCF occupation
-----------------------------------------------------------------------------
1 Screening settings (-IFTHRS, JTDIIS, DIFDEN, times) -9 1 F 1.06D+03 1.06D+03
K-S energy, electrons, error : -237.788968652152 315.9997450495 -2.55D-04
@ 1 -1992.18063685 2.67D+01 -1.99D+03 80 78
Virial theorem: -V/T = 1.919707
@ MULPOP F _1 -0.59; F _2 -0.59; F _1 -0.47; F _2 -0.47; N _1 -1.09; N _2 -1.09; N _1 1.06; N _2 1.06; N _1 0.35; N _2 0.35;
@ C _1 -0.46; C _2 -0.46; C _1 -0.06; C _2 -0.06; C _1 -0.85; C _2 -0.85; C _1 3.60; C _2 3.60; C _1 -0.91; C _2 -0.91;
@ C _1 1.84; C _2 1.84; C _1 1.22; C _2 1.22; C _1 0.03; C _2 0.03; C _1 0.41; C _2 0.41; C _1 0.76; C _2 0.76;
1 Level shift: doubly occupied orbital energies shifted by -2.00D-01
...
I have stopped the calculation for now.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 28 Sep 2019, 05:51

xiongyan21 wrote:
28 Sep 2019, 04:56
I have tried it using Dalton2016.2, and found the output is slightly different
...
The following one-electron property integrals are calculated as requested:
- overlap integrals
- spatial spin-orbit integrals

Center of mass (bohr): 0.000000000000 0.000000000000 0.001198145780
Operator center (bohr): 0.000000000000 0.000000000000 0.000000000000
Gauge origin (bohr): 0.000000000000 0.000000000000 0.000000000000
Dipole origin (bohr): 0.000000000000 0.000000000000 0.000000000000


************************************************************************
************************** Output from HERINT **************************
************************************************************************

Time used in ONEDRV is 1.21 seconds
Time used in HUCKEL is 0.49 seconds
Time used in OVERLAP is 0.14 seconds
Time used in POPOVLP is 0.29 seconds
Time used in DIPLEN is 0.17 seconds
Time used in QUADRUP is 0.33 seconds
Time used in KINENE is 0.27 seconds
Time used in SPNORB is 1.54 seconds
Time used in GABGEN is 1.11 seconds
Total CPU time used in HERMIT: 5.55 seconds
Total wall time used in HERMIT: 5.66 seconds
...,
but it seems the calculation can move on although it may me time-consuming
...

***********************************************
***** DIIS acceleration of SCF iterations *****
***********************************************

C1-DIIS algorithm; max error vectors = 8

Automatic occupation of symmetries with 316 electrons.

Iter Total energy Error norm Delta(E) SCF occupation
-----------------------------------------------------------------------------
1 Screening settings (-IFTHRS, JTDIIS, DIFDEN, times) -9 1 F 1.06D+03 1.06D+03
K-S energy, electrons, error : -237.788968652152 315.9997450495 -2.55D-04
@ 1 -1992.18063685 2.67D+01 -1.99D+03 80 78
Virial theorem: -V/T = 1.919707
@ MULPOP F _1 -0.59; F _2 -0.59; F _1 -0.47; F _2 -0.47; N _1 -1.09; N _2 -1.09; N _1 1.06; N _2 1.06; N _1 0.35; N _2 0.35;
@ C _1 -0.46; C _2 -0.46; C _1 -0.06; C _2 -0.06; C _1 -0.85; C _2 -0.85; C _1 3.60; C _2 3.60; C _1 -0.91; C _2 -0.91;
@ C _1 1.84; C _2 1.84; C _1 1.22; C _2 1.22; C _1 0.03; C _2 0.03; C _1 0.41; C _2 0.41; C _1 0.76; C _2 0.76;
1 Level shift: doubly occupied orbital energies shifted by -2.00D-01
...
I have stopped the calculation for now.
Hi xiongyan, I have no idea about 2016.2 ver, in my case, I run with Dalton 2018.2 ver, so I did not see this error.

xiongyan21
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Re: Calculation of spin orbit coupling constant

Post by xiongyan21 » 28 Sep 2019, 06:06

I should recompile Dalton2018.2 when I am free, because I have upgraded Ubuntu.

Using Dalton2016.2, it seems the calculation can move on, but I am not sure wether it can finish.
Last edited by xiongyan21 on 02 Oct 2019, 00:13, edited 1 time in total.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 28 Sep 2019, 08:43

xiongyan21 wrote:
28 Sep 2019, 06:06
I should recompile Dalton2018.2 when I am free, because I have upgraded Ubuntu.

Using Dalton2016.2, it seems the calculation can move on without errors.
Really, in my case, I do not think it is error, i do not know when I try to run with the small molecule like methane, water, benzene,... everything is fine, however, with the big molecule like BODIPY (boron-dipyrromethene), it keeps repeating like the output I attached, no error occurred but the calculation can not keep moving on.

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magnus
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Re: Calculation of spin orbit coupling constant

Post by magnus » 28 Sep 2019, 15:14

Based on the warnings in the output file:
Min HX interatomic separation is 0.2935 Angstrom ( 0.5547 Bohr)

Min YX interatomic separation is 0.4151 Angstrom ( 0.7843 Bohr)

@ WARNING: Number of short HX and YX bond lengths: 2 11

I'm guessing you do not want to use symmetry generators in your input which generate atoms in addition to those that you give in the input? If so remove "Generators=1 XY" from your molecule input file. Unfortunately, I don't know how to prepare the Dalton input file for what you want to calculate so I can't help with you with that part.

ndhieu92
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Re: Calculation of spin orbit coupling constant

Post by ndhieu92 » 29 Sep 2019, 14:01

magnus wrote:
28 Sep 2019, 15:14
Based on the warnings in the output file:
Min HX interatomic separation is 0.2935 Angstrom ( 0.5547 Bohr)

Min YX interatomic separation is 0.4151 Angstrom ( 0.7843 Bohr)

@ WARNING: Number of short HX and YX bond lengths: 2 11

I'm guessing you do not want to use symmetry generators in your input which generate atoms in addition to those that you give in the input? If so remove "Generators=1 XY" from your molecule input file. Unfortunately, I don't know how to prepare the Dalton input file for what you want to calculate so I can't help with you with that part.
Hi magnus,

Thank you so much for your comments. I will try to do that. Actually, my target is very simple, I need to get the value of spin-orbit coupling constant value as reported in the paper I attached inside my post. Simply explain about my calculation is, I need to calculate spin-orbit coupling constant value which will be used to evaluate for the efficiency of intersystem crossing (transition from excited singlet S1 to excited triplet T1)
As you can refer from this table of paper: https://drive.google.com/file/d/1S_WLY1 ... oItEs/view.

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Re: Calculation of spin orbit coupling constant

Post by xiongyan21 » 01 Oct 2019, 05:32

Dear Dr. Olsen
I think you are correct, because I do not know whether the original input can produce the correct result, and the input should be prepared by a Dalton professional when he absolutely know the aims of the calculation. I am not interested in this calculation, discarded the log file, and will never try it forever.
Very Best Regards!

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