Thank you Professor Postnikov,
Here I will provide two examples of my work
I have a hexagonal structure containing 18 atoms
1. I have substituted one atom with a gaseous one and relaxed it up
to 0.000794 eV/A and 0.00458798  kBar
then I calculated the phonon and fortunately, there is no negative
frequency while the force for the first step is approximated as 0.008174
eV/A

2. I have substituted two atoms with two gaseous ones and relaxed it up
to 0.000549 eV/A and 0.00290065  kBar
then I calculated the phonon and unfortunately, there are frequencies as
-206.30292747012965 while the force for the first step is approximated
as 0.015862 eV/A

For both cases, I have used same inputs as
For relaxation:
MeshCutoff    870 Ry
DM.MixingWeight         0.02
DM.NumberPulay       3
%block kgrid_Monkhorst_Pack
6   0   0   0.0
0   6   0   0.0
0   0   1   0.0
%endblock kgrid_Monkhorst_Pack

For phonon:
MeshCutoff    750 Ry
DM.MixingWeight         0.02
DM.NumberPulay       8
%block kgrid_Monkhorst_Pack
3   0   0   0.0
0   3   0   0.0
0   0   1   0.0
%endblock kgrid_Monkhorst_Pack

I repeated phonon calculation for the second case with
%block kgrid_Monkhorst_Pack
6   0   0   0.0
0   6   0   0.0
0   0   1   0.0
%endblock kgrid_Monkhorst_Pack
and the resulting force for the first step is 0.013928 eV/A

I'm confused about what is happening in these two similar examples.
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SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
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