[QE-users] Normal modes with nat_todo giving unphysical results

[Sriram Goverapet Srinivasan]

Hi All,

I'm trying to compute the vibrational frequencies of adsorbates on a catalyst material. However, when I used 'nat_todo' in ph.x input and specified only adsorbate atoms, I'm getting many more non zero frequencies than the expected '3N' values. Also, these are negative. For example, when I consider H atom adsorbed on Mo2N MXene, I get the following output by setting nat_todo = 1 (corresponding to the adsorbed H atom alone):

freq (    1) =      -3.783307 [THz] =    -126.197541 [cm-1]
freq (    2) =      -3.783307 [THz] =    -126.197534 [cm-1]
freq (    3) =      -2.586423 [THz] =     -86.273795 [cm-1]
freq (    4) =      -0.000000 [THz] =      -0.000013 [cm-1]
freq (    5) =      -0.000000 [THz] =      -0.000011 [cm-1]
freq (    6) =      -0.000000 [THz] =      -0.000010 [cm-1]
..
..
..
freq (   81) =       0.000000 [THz] =       0.000014 [cm-1]
freq (   82) =      27.703969 [THz] =     924.104922 [cm-1]
freq (   83) =      27.703973 [THz] =     924.105062 [cm-1]
freq (   84) =      35.034523 [THz] =    1168.625905 [cm-1]

If I include all atoms in the surface layer together with the H adsorbate in nat_todo (i.e., nat_todo=10), I still get  a similar 'unphysical' result:

# mode   [cm-1]    [THz]      IR
1   -235.75   -7.0675    0.0000
2   -235.75   -7.0675    0.0000
3   -232.81   -6.9793    0.0000
4   -229.08   -6.8675    0.0000
5   -229.08   -6.8675    0.0000
6   -224.95   -6.7437    0.0000
..
..
..
79    314.67    9.4336    0.0000
80    314.67    9.4336    0.0000
81    336.83   10.0978    0.0000
82    916.50   27.4759    0.0000
83    916.50   27.4759    0.0000
84   1158.35   34.7263    0.0000

The moment I remove nat_todo and compute all the frequencies, I'm getting a meaningful result:

# mode   [cm-1]    [THz]      IR
1     -0.00   -0.0000    0.0000
2      0.00    0.0000    0.0000
3      0.00    0.0000    0.0000
4     22.82    0.6841    0.0000
5     22.82    0.6841    0.0000
6     80.49    2.4131    0.0000
7     80.49    2.4131    0.0000
..
..
..
79    541.10   16.2217    0.0000
80    553.66   16.5984    0.0000
81    588.60   17.6459    0.0000
82    924.78   27.7243    0.0000
83    924.78   27.7243    0.0000
84   1170.94   35.1039    0.0000

All calculations are geometry optimized to etot_conv_thr = 1.0D-6  and forc_conv_thr = 1.0D-4 followed by an scf with conv_thr    = 1.D-12.  Following was my ph.in file:
vibra
&inputph
tr2_ph = 1.0d-14
prefix='Ti3C2'
outdir = './'
search_sym = .false.
asr = .true.
alpha_mix(1) = 0.3
# nat_todo = 10
/
0 0 0

Is there something that I'm missing out while doing calculations for a subset of atoms? I'd greatly appreciate the help of the community.

Thank you very much!

Best Regards,
Sriram
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