[DFTB-Plus-User] How to Remove Imaginary Frequencies in DFTB+

[Benjamin Hourahine]

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

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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+

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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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