[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 88, Issue 12
rsaha at icredd.hokudai.ac.jp
rsaha at icredd.hokudai.ac.jp
Fri Dec 24 05:43:21 CET 2021
Hello Everyone,
Thank you Dr. Hourhine. I tried your suggestions and it worked well.
I have a few small queries,
(1) I am considering this sentence, "Also, you might want to relax the
geometry with tighter tolerances than the default settings" as, you mean
to calculate the "hessian" calculation using tighter "SCCTolerance"
For optimisation, I have used "SCCTolerance = 1e-6".
For the hessian calculation I have used,
(a) SCCTolerance = 1e-7: gave 3 imaginary frequencies followed by 6 zero
frequencies (the translational and vibrational) and then the positive
frequencies.
(b) SCCTolerance = 1e-8: gave first 6 zero frequencies (the
translational and vibrational) and then all positive frequencies.
So, does it mean that I have to choose the "SCCTolerance" for the
frequency calculation carefully? Or optimisation with tigther "
SCCTolerance" is required? I like to hear opinions about this point.
(2) Thank you again for the perl command. It was very helpful.
Regards
Ranajit
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> 1. Re: How to Remove Imaginary Frequencies in DFTB+
> (Benjamin Hourahine)
>
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 22 Dec 2021 12:49:39 +0000
> From: Benjamin Hourahine <benjamin.hourahine at strath.ac.uk>
> To: User list for DFTB+ related questions
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: Re: [DFTB-Plus-User] How to Remove Imaginary Frequencies in
> DFTB+
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> Hello Ranajit,
>
> There is an option to project out translational and (if non-periodic)
rotational components of the hessian, which should remove most of the
usual cause of imaginary modes. Look for RemoveTranslation and
RemoveRotation keywords in the manual. Also, you might want to relax the
geometry with tighter tolerances than the default settings.
>
> We will fix the formatting for the xyz files in the next release, but
in the meantime a quick way to process these files to add space is by
replacing "-" by " -" in the files with a script. A one line perl
command would be
>
> perl -i.bak -p -e "s/-/ -/g" file.xyz
>
> Regards
>
> Ben
>
> Dr. B. Hourahine, SUPA, Department of Physics,
> University of Strathclyde, John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK.
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> 2013/4 THE Awards Entrepreneurial University of the Year
> 2012/13 THE Awards UK University of the Year
>
> The University of Strathclyde is a charitable body,
> registered in Scotland, number SC015263
> ________________________________
> From: DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de
> on behalf of rsaha at icredd.hokudai.ac.jp <rsaha at icredd.hokudai.ac.jp>
> Sent: 22 December 2021 03:21
> To: dftb-plus-user at mailman.zfn.uni-bremen.de <dftb-plus-user at mailman.
zfn.uni-bremen.de>
> Subject: [DFTB-Plus-User] How to Remove Imaginary Frequencies in DFTB+
>
> CAUTION: This email originated outside the University. Check before
clicking links or attachments.
>
> Hello Everyone,
>
> Recently, I am trying to do frequency calculations (Second derivative
+
> modes) using DFTB+18.2. The systems have a total of 722 atoms.
>
> (1) After the calculation, I have found that there are some imaginary
> frequencies. I am considering modes from 7th and so on.
> """
> Vibrational modes (cm-1):
> 1 -21.22
> 2 -20.11
> 3 -16.83
> 4 -15.29
> 5 -13.92
> 6 -12.07
> 7 -11.08
> 8 -9.81
> 9 -8.27
> 10 -6.61
> 11 -5.34
> 12 2.29
> 13 4.83
> 14 6.89
> 15 9.37
> """
>
> Is there any general procedure to remove these imaginary frequencies?
> I have used G16/Gview6 before which was very easy to work with
imaginary
> frequencies. I want to know what to do with DFTB+ outputs and I guess
it
> will not be straightforward as G16/Gview.
>
> Another part, the imaginary frequencies (from 7th and so on) are very
> small (< 50cm-1). Is it required to remove them? Generally, I remove
all
> imaginary frequencies in my calculations. Please let me know your
> opinion.
>
>
> (2) In some part of the mode_**.xyz files, the XYZ coordiantes look
like
> this,
> """
> H -44.267149 -6.948083 0.672858
> H -43.163722-10.245054 3.204615
> C -47.879462 -0.613343 11.689011
> """
>
> As you can see there is no space between the x and y coordinate in the
> second line, which causes problems in visualising these modes with
> Chemcraft (VMD works well though). Is there any way to clean this
format
> and make it readable using Chemcraft?
>
> Thank you all for your time and reading.
>
> Regards
> Ranajit
>
>
>
>
>
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