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Geometry convergance problems for organometallic compound
From NWChem
Viewed 874 times, With a total of 8 Posts

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1:13:00 AM PDT  Tue, Apr 30th 2019 

Dear NWChem developers and users:
I have been using NWChem 6.6 to perform computations on organometallic compounds using B3LYP/Lanl2DZ/6311+G* for a couple of months now but I keep running in geometry convergence issues, i.e. I end up with one or two imaginary frequencies. I know this topic has been discussed numerous times in this forum but all solutions that seemed to work for the other users did not work for me. First of all here is my input file
start ProductCompound+Pd_ActivNewTry
title "ProductCompound+Pd_Activ in 6311+g* basis set"
scratch_dir ../../../../var/scratch/user
memory total 8000 mb
charge 1
geometry units angstroms print xyz autosym
C 0.84169 4.67838 0.78686
C 1.65397 3.38660 0.96403
H 1.71396 3.11420 2.02404
H 2.68067 3.53152 0.62818
C 0.81108 5.06104 0.70418
H 1.82691 5.25146 1.06680
H 0.24681 5.98894 0.84871
C 0.59057 4.45649 1.29716
H 1.18915 5.36596 1.17793
H 0.58450 4.22342 2.36829
C 1.03586 2.19919 0.15858
C 0.16400 3.91760 1.50747
H 0.13525 4.18115 2.57003
C 1.23527 3.30783 0.50083
H 2.25590 3.13864 0.86420
C 1.00137 2.63356 1.33562
C 0.40263 1.99950 0.73850
C 1.26997 3.69073 0.99150
H 2.02947 2.81257 1.66299
H 1.85682 4.60796 1.10790
H 1.78896 2.93546 1.59039
H 0.26814 1.91138 1.82192
H 0.62254 1.83117 1.97726
H 1.32011 5.47621 1.36413
C 2.03374 1.02677 0.30303
N 1.65887 0.28979 0.39970
O 3.23714 1.27466 0.35105
C 2.68492 1.24806 0.05181
Pd 0.18915 1.02023 0.40189
C 0.19606 3.93530 0.45343
C 0.93663 5.05841 0.77117
N 0.77952 2.74485 0.21089
H 3.49750 1.29078 0.68187
H 3.14971 0.89072 0.97802
C 2.32714 4.94388 0.83541
C 2.11951 2.61368 0.27843
C 2.92018 3.71491 0.58740
H 0.43566 5.99866 0.96547
H 2.93777 5.80587 1.07986
H 3.99642 3.59503 0.63422
H 0.88556 3.96331 0.39216
C 1.23672 0.78444 0.35938
C 1.99822 0.17545 1.42220
C 1.56525 0.36838 0.96422
C 2.90352 0.83525 1.21601
C 2.42046 0.72670 1.18037
C 3.09822 1.33314 0.10341
H 1.83795 0.53558 2.43275
H 1.14869 0.86934 1.82439
H 3.44415 1.25444 2.05408
H 2.63506 1.06956 2.18525
O 3.91464 2.33607 0.41531
C 4.68995 2.99342 0.60493
H 5.37414 2.28919 1.08103
H 4.03828 3.45909 1.34701
H 5.25736 3.75752 0.08147
end
basis
H library 6311+G*
O library 6311+G*
N library 6311+G*
C library 6311+G*
Pd library lanl2dz_ecp
end
ecp
Pd library lanl2dz_ecp
end
stepper
maxiter 100
end
scf
thresh 1.0 d8
end
dft
xc b3lyp
grid fine
tolerances tight
convergence energy 1.0d8
iterations 100
end
task dft optimize
task dft freq
This was my last attempt to reach convergence, without success. Before I also tried
1. the "default" driver module with settings tight
2. did computations with and without "autosym"
3. changing the structure randomly to approach the minimum from different directions
4. use the normal vectors of the imaginary frequencies to change the structure along these normal vectors
All attempts without success and I always end up with imaginary frequencies (about 60 cm^1). Does someone has another idea what to try and could this also come from an incorrect compilation of the NWChem code and corresponding libraries?
Best regards,
StarkEffect




Forum Regular
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Posts 291


6:41:33 PM PDT  Tue, Apr 30th 2019 

The following reference from Tang, et al. may be helpful but it might be unsuitable in your case.
The Electrolyte Genome project: A big data approach in battery materials discovery.
Computational Materials Science. 103(2015) 5667
"The results, shown in Fig. 4, demonstrate that if the frequency is very low (<39.0 cm1), a highaccuracy frequency calculation can remove up to 42% of the imaginary frequencies. However, high accuracy reoptimization is less helpful for larger imaginary frequencies. In contrast, the two molecular geometry perturbation strategies work extremely well: they remove at least 21 out of the 24 imaginary frequencies for the whole range of imaginary frequencies."

Edited On 7:02:34 PM PST  Sat, Nov 30th 2019 by Xiongyan21




Just Got Here
Threads 1
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2:29:19 AM PDT  Thu, Jun 13th 2019 

Dear Xiongyan21 and NWChem developers:
Thanks for your reply. Unfortunetely, I was unable to resolve the problem posted above.
Additionally, I tested other quantum chemistry codes with their implementation of the same level of theory but in these codes the geometry optimization and subsequent frequency computations revealed that the structure has converged and is a local minimum.
To double check I asked a friend to run the same computation on another machine with the newest NWChem version. The computation also failed.
Therefore, my followup question: is anything known about numerical inaccuracies for some special cases? Are there ways to check for probelms or even resolve these?
Best regards,
StarkEffect




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Threads 61
Posts 291


5:00:24 PM PST  Sat, Nov 23rd 2019 

Somebody recommended the decrease of the symmetry, e.g., using C1, to eliminate it. I have just tried thiabendazole, which also can be considered as to be planar even in C1, using GAMESS with 6311++G(2d,2p) and b3lyp, and the approximate 55 cm1 imaginary frequency has been removed during HF vibrational anaysis with the warning meaning it is not a true stationary point even if the convergence criteria are met, thus HESSIAN analysis is not rigorious.
The obtained THz results with GAMESS exhibits two peaks in the range of 02.0 THz, and not greater than 14 cm1 compared with the two chief peaks in PLS model investigation of thiabendazole based on THz spectrum , assuming 1THZ =33.33 cm1.
MODE FREQ(CM**1) SYMMETRY RED. MASS IR INTENS.
1 0.026 A ... 0.000000
2 0.004 A ... 0.000000
3 0.034 A ... 0.000000
4 33.966 A ... 0.000687
5 50.002 A ... 0.010410
...
If the imaginary frequency has not been eliminated, it gives
MODE FREQ(CM**1) SYMMETRY RED. MASS IR INTENS.
1 55.684 A" ... 0.105512
2 1.891 A" ... 0.090056
3 0.114 A" ... 0.001076
4 0.052 A' ... 0.000036
5 0.034 A' ... 0.000001
6 0.814 A' ... 0.010790
7 1.182 A" ... 0.000087
8 66.596 A" ... 0.068779
...
1 2 3 4 5
FREQUENCY: 55.68 I 1.89 0.11 0.05 0.03
SYMMETRY: A" A" A" A' A'
REDUCED MASS: ...
IR INTENSITY: 0.10551 0.09006 0.00108 0.00004 0.00000
...
NWCHEM SCF and 631+G(d) frequency analysis gives
Normal Eigenvalue  Projected Infra Red Intensities
Mode [cm**1]  [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
      
1 0.000  0.000331 0.008 0.323 0.196
2 0.000  0.002410 0.056 2.350 1.424
3 0.000  0.000866 0.020 0.844 0.512
4 0.000  0.000963 0.022 0.939 0.569
5 0.000  0.000105 0.002 0.102 0.062
6 0.000  0.000074 0.002 0.073 0.044
7 92.624  0.000461 0.011 0.449 0.272
8 99.156  0.000909 0.021 0.886 0.537
...
Of course this cannot agree with current published experimental THz spectra of this molecule'.

Edited On 12:02:43 AM PST  Tue, Jan 21st 2020 by Xiongyan21




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8:11:04 PM PST  Sat, Nov 30th 2019 

With GAMESS, the 6311++G(2d,2p) optimized Carbendazim can give the following peaks, when doing vibrational analysis using the same basis set and HF, even having the warning.
MODE FREQ(CM**1) SYMMETRY RED. MASS IR INTENS.
1 0.013 A ... 0.000000
2 0.008 A ... 0.000000
3 0.006 A ... 0.000000
4 37.138 A ... 0.002125
5 55.879 A ... 0.007225
6 90.644 A ... 0.029414
Please note, after an mini basis set Monte Carlo search first, the imaginary frequency of this molecule in later vibrational analysis after an geometry optimization has been eliminated.
...

Edited On 12:47:33 AM PST  Wed, Dec 25th 2019 by Xiongyan21




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12:13:34 AM PST  Wed, Dec 25th 2019 

The 6311G++(2d,2p) vibrational analysis of the same functional, i.e., b3lyp, same basis set optimized thiabendazole gives the following using GAMESS.
1 37.366 A
2 7.082 A
3 0.027 A
4 0.003 A
5 0.035 A
6 6.201 A
7 15.991 A
8 65.706 A
Please not there is an imaginary frequency existing, and the frequencies mismatching.
The previously did b3lyp 631G+(d,p) optimized Cs thiabendazole gives the following during the RHF Hessian analysis using the same basis set even using Cs symmetry and the same functional
MODE FREQ(CM**1)
1 0.046 A'
2 0.020 A
3 0.008 A'
4 36.068 A
5 52.861 A' ,
but 631G+(d.p) optimized thiabendazole gives the following during the RHF b3lyp Hessian analysis using the same basis set with C1
MODE FREQ(CM**1)
1 33.580 A
2 4.732 A
3 0.055 A
4 0.047 A
5 0.022 A
6 5.641 A
7 14.790 A
8 67.181 A

Edited On 4:35:52 PM PST  Thu, Dec 26th 2019 by Xiongyan21




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4:39:18 PM PST  Thu, Dec 26th 2019 

The 6311G++(2d,2p) b3lyp optimized carbendazim?whose initial geometry was obtained by an mini basis set Monte Carlo search first, gives no imaginary frequency when doing vibrational analysis using the same functional and same basis set, but the number and positions of peaks changes when compared with the HF result.
All the DFT and HF vibrational analyses employs analytical methods.

Edited On 8:09:21 PM PST  Sun, Jan 5th 2020 by Xiongyan21




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8:23:38 PM PST  Sun, Jan 5th 2020 

It seems only HF Hessian analysis using GAMESS with the default solver setup can be compared with the experimental data in peak numbers and positions in the THz region.
For example, in the case of alanine, the RHF seminumerical and analytical methods with 6311G++(2d,2p) of the geometry obtained by mp2 optimization with the almost same basis set, having a warning meaning the analysis is not very rigorous because of the geometry obtained by optimization is not a true stationary point. The analytical method gives
MODE FREQ(CM**1) ... IR INTENS.
1 0.015 A 0.000000
2 0.008 A 0.000000
3 0.016 A 0.000000
4 61.236 A 0.032632
5 79.238 A 0.013808
which can be compared with the data of D or L alanine in Terahertz absorption spectra of L,D,and DLalanine and their application to determination of enantiomeric composition, in peak numbers and positions, but the mp2 seminumerical
Hessian analysis with the same basis set and geometry, with no such warning, renders
MODE FREQ(CM**1) ... IR INTENS.
1 2.723 A 0.057955
2 2.307 A 0.101703
3 1.393 A 0.010289
4 0.149 A 0.000367
5 0.340 A 0.001699
6 2.174 A 0.005833
7 56.927 A 0.082500
The b3lyp analysis with the default analytical hessian input setup gives
MODE FREQ(CM**1) ... IR INTENS.
1 64.741 A 0.012959
2 38.942 A 0.034262
3 0.098 A 0.000032
4 0.007 A 0.000000
5 0.021 A 0.000000
6 4.677 A 0.072961
7 71.778 A 0.191482

Edited On 6:04:16 PM PST  Wed, Jan 8th 2020 by Xiongyan21




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Posts 291


8:28:18 PM PST  Sun, Jan 5th 2020 

In the case of Asprin, with rich Thz peaks, it seems also RHF frequency analysis perhaps can be compared with the experimental NIST THZ spectrum, whereas the one using B3lyp mismatches. Toward precise assignment of THz spectra by DFT suggests correction methods to improve the gaps between the theoretically calculatedted and the experimentally obtained.
Since the gaps between the values of the theoretically calculated and the experimentally obtained are obvious with the default GAMESS input setup, according to the above article, all those mentioned here are only for educational usage, and I am not interested in any other molecule's THz quantum chemical calculations.

Edited On 10:43:08 PM PST  Sun, Jan 5th 2020 by Xiongyan21



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