two-photon:the TPA cross section

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Gemmagemma
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two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 09:47

Hi, everybody,

I’m a new learner of Dalton and two-photon. I want to calculate the TPA cross section by Dalton 2.0, the code I have used are in the follows:
**DALTON INPUT
.DIRECT
.RUN RESPONSE
!.RUN ALL
**WAVE FUNCTIONS
.DFT
B3LYP
**RESPONSE
*QUADRATIC
.TWO-PHOTON
.ROOTS
6
**END OF

In this work, I just want to repeat the results of the previous literature. My question is we have the same bond length after the optimization and then I used the above Dalton input files to calculate the TPA cross section. However, this didn’t get the same result as the literature.
My result:
E=2.41 3.09 3.98 4.22 4.25 4.71

The previous literature:
E= 2.16 2.61 3.25 3.37 3.54 3.78
The main problem occurred. Why the energies of my results are much higher than those of the previous literature? Are there any errors in my Dalton input or anywhere else?
Please, could anybody tell me the reason?
Thanks!
Gemma

arnfinn
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Re: two-photon:the TPA cross section

Post by arnfinn » 18 Aug 2014, 09:58

First of all you should use Dalton2013 instead of Dalton 2.0 (the GM numbers are wrong in Dalton 2.0, so you have to use the a.u. numbers).

Your dalton input file looks OK, as far as I can see. Are you sure the structures are identical? Can you provide us with the molecule input and a reference to the article you are comparing your numbers with?

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 10:17

Dear Arnfinn:
Thanks a lot for your fast reply. In your reply, "the GM numbers are wrong in Dalton 2.0",what does it mean? In my calculation, after the computation of the dalton, we would have calculate by a Equation to get the final TPA cross section, the article is from a chinese journal ,so I'd like to provide my molecule input to you. Thanks for your further help!
BASIS
6-31G
1r
a.u.
4 0
6. 15
c -7.201321 -1.219773 -.316121
c -5.790198 1.052049 -.642223
c -3.171917 1.038153 -.592200
c -1.827317 -1.230663 -.203767
c -3.200310 -3.478024 .131733
c -5.826453 -3.490729 .082112
c -11.296623 1.065246 -.875136
c -11.802937 2.620554 1.513998
c -11.211298 -3.589372 .070079
c 4.747009 .381709 -.315076
c 6.127257 2.623678 -.648868
c 8.760406 2.607796 -.590072
c 10.041094 .319720 -.191043
c 8.676877 -1.938062 .153957
c 6.049930 -1.903431 .092894
1. 18
h -6.755062 2.834956 -.922754
h -2.112060 2.772837 -.841860
h -2.149871 -5.213283 .431089
h -6.811310 -5.263814 .342257
h -10.337328 2.253678 -2.268329
h -13.110663 .531752 -1.711444
h -12.854714 1.475331 2.894251
h -10.009470 3.196932 2.387771
h -13.615825 5.929431 2.098748
h -13.236124 -3.201835 .007301
h -10.768139 -4.399729 1.928569
h -10.781757 -5.018552 -1.374140
h 5.088646 4.365268 -.944705
h 9.828389 4.334100 -.818559
h 9.693612 -3.677886 .494537
h 4.967047 -3.619157 .363934
h 15.109173 -2.480586 .461206
h 15.209211 2.977779 -.567359
7. 4
n -9.828629 -1.232739 -.379641
n .827565 -1.438847 -.113614
n 2.075100 .623119 -.413293
n 12.756700 .233767 -.371866
8. 3
o -13.269710 4.792020 .686093
o 13.677285 -1.737009 1.378679
o 13.765665 2.664058 .556076

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 10:21

arnfinn wrote:First of all you should use Dalton2013 instead of Dalton 2.0 (the GM numbers are wrong in Dalton 2.0, so you have to use the a.u. numbers).

Your dalton input file looks OK, as far as I can see. Are you sure the structures are identical? Can you provide us with the molecule input and a reference to the article you are comparing your numbers with?
The optimized molecular structure is as follows:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 -3.792454 -0.634097 -0.194241
2 6 0 -3.042260 0.558564 -0.374670
3 6 0 -1.663456 0.550768 -0.340938
4 6 0 -0.951890 -0.640763 -0.117964
5 6 0 -1.682216 -1.818894 0.069419
6 6 0 -3.066650 -1.825873 0.035630
7 7 0 -5.172531 -0.641714 -0.244331
8 6 0 -5.945746 0.572255 -0.462143
9 6 0 -6.218552 1.363056 0.818726
10 8 0 -6.989826 2.496410 0.436553
11 6 0 -5.901658 -1.871841 0.024185
12 7 0 0.445931 -0.752160 -0.059775
13 7 0 1.085639 0.319066 -0.232650
14 6 0 2.491222 0.193038 -0.168917
15 6 0 3.224254 1.366326 -0.373129
16 6 0 4.611962 1.360167 -0.333924
17 6 0 5.289739 0.165124 -0.081305
18 6 0 4.565344 -1.017874 0.125108
19 6 0 3.182229 -1.002183 0.084049
20 7 0 6.719604 0.117283 -0.160827
21 8 0 7.195950 -0.866164 0.753239
22 8 0 7.245329 1.373057 0.255097
23 1 0 -3.547207 1.500704 -0.537720
24 1 0 -1.105579 1.467453 -0.480677
25 1 0 -1.133528 -2.737210 0.243996
26 1 0 -3.585221 -2.761965 0.185315
27 1 0 -5.443780 1.221460 -1.181662
28 1 0 -6.903259 0.301013 -0.912056
29 1 0 -6.762143 0.727812 1.532577
30 1 0 -5.268194 1.656303 1.282684
31 1 0 -7.144818 3.036685 1.216105
32 1 0 -6.969844 -1.671034 -0.043697
33 1 0 -5.693408 -2.265857 1.026165
34 1 0 -5.657949 -2.653082 -0.705257
35 1 0 2.680182 2.284427 -0.560059
36 1 0 5.173924 2.270297 -0.481436
37 1 0 5.099262 -1.934018 0.331600
38 1 0 2.612753 -1.906940 0.248756
39 1 0 7.915616 -1.279841 0.262876
40 1 0 7.971862 1.513397 -0.362865
---------------------------------------------------------------------

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 10:22

arnfinn wrote:First of all you should use Dalton2013 instead of Dalton 2.0 (the GM numbers are wrong in Dalton 2.0, so you have to use the a.u. numbers).

Your dalton input file looks OK, as far as I can see. Are you sure the structures are identical? Can you provide us with the molecule input and a reference to the article you are comparing your numbers with?
Dear Arnfinn:
Thanks a lot for your fast reply. In your reply, "the GM numbers are wrong in Dalton 2.0",what does it mean? In my calculation, after the computation of the dalton, we would have calculate by a Equation to get the final TPA cross section, the article is from a chinese journal ,so I'd like to provide my molecule input to you. Thanks for your further help!
BASIS
6-31G
1r
a.u.
4 0
6. 15
c -7.201321 -1.219773 -.316121
c -5.790198 1.052049 -.642223
c -3.171917 1.038153 -.592200
c -1.827317 -1.230663 -.203767
c -3.200310 -3.478024 .131733
c -5.826453 -3.490729 .082112
c -11.296623 1.065246 -.875136
c -11.802937 2.620554 1.513998
c -11.211298 -3.589372 .070079
c 4.747009 .381709 -.315076
c 6.127257 2.623678 -.648868
c 8.760406 2.607796 -.590072
c 10.041094 .319720 -.191043
c 8.676877 -1.938062 .153957
c 6.049930 -1.903431 .092894
1. 18
h -6.755062 2.834956 -.922754
h -2.112060 2.772837 -.841860
h -2.149871 -5.213283 .431089
h -6.811310 -5.263814 .342257
h -10.337328 2.253678 -2.268329
h -13.110663 .531752 -1.711444
h -12.854714 1.475331 2.894251
h -10.009470 3.196932 2.387771
h -13.615825 5.929431 2.098748
h -13.236124 -3.201835 .007301
h -10.768139 -4.399729 1.928569
h -10.781757 -5.018552 -1.374140
h 5.088646 4.365268 -.944705
h 9.828389 4.334100 -.818559
h 9.693612 -3.677886 .494537
h 4.967047 -3.619157 .363934
h 15.109173 -2.480586 .461206
h 15.209211 2.977779 -.567359
7. 4
n -9.828629 -1.232739 -.379641
n .827565 -1.438847 -.113614
n 2.075100 .623119 -.413293
n 12.756700 .233767 -.371866
8. 3
o -13.269710 4.792020 .686093
o 13.677285 -1.737009 1.378679
o 13.765665 2.664058 .556076

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 11:06

arnfinn wrote:First of all you should use Dalton2013 instead of Dalton 2.0 (the GM numbers are wrong in Dalton 2.0, so you have to use the a.u. numbers).

Your dalton input file looks OK, as far as I can see. Are you sure the structures are identical? Can you provide us with the molecule input and a reference to the article you are comparing your numbers with?
Dear Arnfinn:
I have another question. Does the difference of the Energy is related to the different versions of Dalton?

arnfinn
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Re: two-photon:the TPA cross section

Post by arnfinn » 18 Aug 2014, 11:18

Gemmagemma wrote: I have another question. Does the difference of the Energy is related to the different versions of Dalton?
Most probably not, except if you are running into a bug that has been fixed in the later versions (probably not, but very hard to know).

Can you give us a link to the article, even if it is in Chinese?

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 11:32

arnfinn wrote:
Gemmagemma wrote: I have another question. Does the difference of the Energy is related to the different versions of Dalton?
Most probably not, except if you are running into a bug that has been fixed in the later versions (probably not, but very hard to know).

Can you give us a link to the article, even if it is in Chinese?
Dear Arnfinn:
Thanks for your reply. The article address is as follows: (Their article language is English)

http://cpb.iphy.ac.cn/EN/abstract/abstract22146.shtml

In our calculations, each step can be carried out smoothly and does not show the error. However, the results are different. This problem has been bothering me for a long time. My problem is mainly at the calculated energy of our results are different from theirs which could cause the different wavelengths of two-photon absorption(In fact, our energy is higher). Then,we'll have the difficulty to make contrast with their results.

Thanks for your help!
Gemma

bast
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Re: two-photon:the TPA cross section

Post by bast » 18 Aug 2014, 11:37

hi,
but since the original authors have used Dalton 2.0, i would
ask the article authors for the their structure data and Dalton input files. then you should
be able to either reproduce exactly or identify the difference.
radovan

lyzhao
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Re: two-photon:the TPA cross section

Post by lyzhao » 18 Aug 2014, 11:39

Gemmagemma wrote:
arnfinn wrote:the GM numbers are wrong in Dalton 2.0, so you have to use the a.u. numbers.
As I remember, the GM numbers are wrong in Dalton 2011 not in Dalton 2.0 which does not output GM numbers.
This bug has been fixed in Dalton 2013. please use Dalton 2013
The inconsistentness between your result and the literature may arise from different basis sets, the damping factor, or other factors.
If you attach your dalton 2.0 output file (do not post directly) and show how you calculate your GM, more help would be given.
This paper http://dx.doi.org/10.1016/j.cplett.2012.07.034 may be useful for you.

Best.
Lan

Gemmagemma
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Re: two-photon:the TPA cross section

Post by Gemmagemma » 18 Aug 2014, 11:47

bast wrote:hi,
but since the original authors have used Dalton 2.0, i would
ask the article authors for the their structure data and Dalton input files. then you should
be able to either reproduce exactly or identify the difference.
radovan
Dear radovan:
Thangks for your reply and your future help on my problem. The optimized bond length of our results is nearly the same as the article, so the mistake may be appeared in my .mol file or the Dalton input file which have cause the different of the energy. My optimized molecular structure, the .mol file and the Dalton input file are given above.

Thanks!
Gemma

lyzhao
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Re: two-photon:the TPA cross section

Post by lyzhao » 18 Aug 2014, 11:53

please note that if you use dalton 2.0, where the output D has included 1/30 factor,
the expression in eq.4 in your given paper should have a prefactor of 8 not 4/15.

best
Lan

peppelicari
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Re: two-photon:the TPA cross section

Post by peppelicari » 28 Feb 2016, 19:23

Dear all,
I'm also having some issue in converting TPA values. I'm using Dalton 2015 and I can calculate correctly the 'Df', 'Dg' and 'D' values (transition probabilities in a. u. starting from the transition tensor). Now, I tried to calculate 'sigma' using the formula specified in the TPA run output:
8*pi^3*alpha^2*hbar/e^4 * E^2*D (a.u.)
but I do not get the same value like the tabulated sigma in the TPA summary (after conversion of a.u. in GM). I think I do not interpret the parameters in the formula correctly. Could you please rewrite this equation here in a clearer way saying what is what and the units? I really would be glad for this.
Other question, where is the FWHM specification in the formula?

Thanks in advance and have a nice evening!
Regards,
Giuseppe

arnfinn
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Re: two-photon:the TPA cross section

Post by arnfinn » 28 Feb 2016, 22:09

The pre-factor has been corrected "recently" (some years ago), and there was a factor (1/2)^2 missing (corrected in the computed TPA cross section, but probably not in the equation printed in the output). The FWHM is set to 0.1 eV, and cm is used instead of m (so you end up with the units cm^4 · s · photon^{−1}). You might want to take a look at this article http://pubs.acs.org/doi/abs/10.1021/ct501113y (section 4.2, and especially equation 93) for some details about how to compute TPA cross sections. This article might also be helpful: http://pubs.rsc.org/en/Content/ArticleL ... ivAbstract

peppelicari
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Re: two-photon:the TPA cross section

Post by peppelicari » 29 Feb 2016, 11:17

Dear Arnfinn,
thanks indeed for the paper, there the formula is clear to me.
Still I have some doubts on the formula written in the output of the calculation. Here I write down what I do and do not understand from the previous formula, 8*pi^3*alpha^2*hbar/e^4 * E^2*D (a.u.):

8*pi^3 : constant value
alpha : 0.0072973525 [dimensionless]
hbar : 6.582119514*10^-16 [eV*s] (if everything is in a.u. shouldn't hbar = 1 ?)
e : 1.6021766208*10^-19 [C^4] (elementary charge, again shouldn't e = 1?]
E: photon energy or excitation energy? In eV or a.u.?
D: transition probability in a.u., as calculated from the sum over the TPA transition tensor elements.

Is the 'e^4' the only factor which the rest of the expression is divided by?
Does the inclusion of the FWHM mean dividing the whole expression by (pi*FWHM) ? (FWHM expressed in eV or a.u.?)

Sorry for this, but I was not able to clarify by myself yet, the reported formula looks quite different from the papers ones. I guess it is the result of the various simplifications of the expression but, I got quite stacked on it.

Thanks again for the help if it is possible and wish you a nice day!
Regards,
Giuseppe

arnfinn
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Re: two-photon:the TPA cross section

Post by arnfinn » 04 Mar 2016, 11:55

In my personal au2GM script I use the following:

Code: Select all

bohr=5.291772108e-9     # cm
alpha=0.007297352568    # -
c=2.99792458e10         # cm/s
eV2au=0.03674932379     # au/eV
pi=math.pi              # -

# or with scipy.constants:
#from scipy.constants import *
#bohr=1e2*physical_constants['Bohr radius'][0]
#eV2au=physical_constants['electron volt-hartree relationship'][0]
#c=c*100 # to make the speed of light in cm/s

def au2GM(exi_ev,sigma_au):
    # input: excitation energy in eV, 
    lorentzian=0.0036749326 # au
    const=1e50*8*(pi**2)*alpha*(bohr**5)/(c*lorentzian*4)
    exi_au=exi_ev*eV2au
    sigma_GM=const*exi_au**2*sigma_au # this is missing a factor 1/2^2 ...
    return sigma_GM
This is what is used inside Dalton:

Code: Select all

      PARAMETER (AU_TO_GM=1.0D50*8*PI**2*ALPHAC*
     &     (XTANGM10*1.0D2)**5 /(CCM*1.0D2*0.0036749326))
where the constants used are taken from codata.h:

Code: Select all

ALPHAC  = 1.0D0/CVEL
CVEL    = CCM*XTANGM10*EMASS/(HBAR)
XTANGM10= XTANG*1.0D-10
XTANG   = 0.5291772083D0
Does it make any sense?:)

peppelicari
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Re: two-photon:the TPA cross section

Post by peppelicari » 04 Mar 2016, 13:57

Dear Arnfinn,
it is clear indeed, I can reproduce the Dalton output values starting from the TPA transition tensor.

I would have one more question to ask, something I'm not 100% sure. As it is pointed out in the paper that you posted (http://pubs.rsc.org/en/Content/ArticleL ... ivAbstract) for an experiment using a single laser beam the N factor should be 16 if using eq. (1). Afterwards I got a bit confusing when came to the point of which value to use with respect to Dalton output and implementation. What I understood if that if I want to compare single beam experiment with Dalton calculation I have to use N = 4 in eq. (1) and the insert TPA strength (sigmaTPA) as printed in the Dalton output (the "D" parameter [a.u.]). Is that correct?

I thank you again for your kind reply and wish you a nice afternoon!
Regards,
Giuseppe

maartenbeerepoot
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Re: two-photon:the TPA cross section

Post by maartenbeerepoot » 04 Jun 2016, 09:14

What I understood if that if I want to compare single beam experiment with Dalton calculation I have to use N = 4 in eq. (1)
That is correct.
insert TPA strength (sigmaTPA) as printed in the Dalton output (the "D" parameter [a.u.])
That is almost correct. Indeed you need to use the "D" parameter [a.u.] in the Dalton output. However, this is not sigmaTPA but deltaTPA.

Regards,
Maarten Beerepoot

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