Re: [SIESTA-L] strange force in phonon calculation

[Andrei Postnikov]

Dear Ziba,it seems that you are randomly trying different options.Try to be 
more systematic.MeshCutoff of 870 Ry seems to be an overkill -but certainly not 
an error; if your tests show that you need as much as that, so be it.Did you 
have a look at your structures with visualisation tools - is everything as it 
should be, no obvious structure error?If your imaginary frequency is genuine 
and reproducible,I'd look at the eigenvector of this mode, give a small 
displacementto atoms along this eigenvector, and make the relaxation again. The 
total energy ought to be lower than in your initial starting point;this is the 
idea of an imaginary frequency: you displace the atomswithin the corresponding 
mode, and the energy goes down.Hence you were not at the equilibrium; try 
better.No way around.Best regardsAndrei Postnikov
- Ziba Torkashvand  a écrit :
>
Thank you Professor Postnikov,Here I will provide two examples of my workI have 
a hexagonal structure containing 18 atoms1. I have substituted one atom with a 
gaseous one and relaxed it up to 0.000794 eV/A and 0.00458798  kBarthen 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  kBarthen 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 asFor relaxation:MeshCutoff870 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: MeshCutoff750 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.

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] strange force in phonon calculation

[Ziba Torkashvand]

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:
MeshCutoff870 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:
MeshCutoff750 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.
[image: image.gif]
[image: Mailtrack]

Sender
notified by
Mailtrack

09/07/21,
01:54:22 AM

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] strange force in phonon calculation

[Andrei Postnikov]

Dear Ziba,probably you'll need to explain better what's your problem.> Once I'm 
relaxing my structure up to 0.0004 eV/Ang after the first MD step of phonon 
calculation > without any displacement the maximum force will be 0.002 eV/Ang 
"The first step without any displacement" is just calculation of your relaxed 
structure.If it is as you say then either it was not fully relaxed, or you 
changed some parametersbetween the two calculations. (A guess: either the 
coordinates are not those from the relaxed case,or the density matrix taken was 
not converged).> but still there is no negative frequency.- what you mean, 
"still"? And how do you know "there is no negative frequency" if you've just 
done "the first step without any displacement"?> This time I've relaxed my 
structure up to 0.0002 eV/Ang but in the first step I'm receiving 0.015 eV/Ang- 
see above> which is leading to the negative frequencies.- for what I know, 
negative frequencies are are hint that the starting point for a phonon 
calculationwas not at the local minimum, i.e., the relaxation was not good. How 
negative are your frequencies?> In the successful phonon calculations I just 
lowered the number of kpoint in the Monkhorst pack for phonon calculation > but 
this time even the kpoints are the same as relaxation input.- reducing the 
k-mesh is certainly not a working recipe for getting phonons right; you've just 
had luck.Best regardsAndrei Postnikov
- Ziba Torkashvand  a écrit :
>
Hello everyone,I'm trying to do phonon calculation for some hexagonal 
structures.Once I'm relaxing my structure up to 0.0004 eV/Ang after the first 
MD step of phonon calculation without any displacement the maximum force will 
be 0.002 eV/Ang but still there is no negative frequency.This time I've relaxed 
my structure up to 0.0002 eV/Ang but in the first step I'm receiving 0.015 
eV/Ang which is leading to the negative frequencies.In the successful phonon 
calculations I just lowered the number of kpoint in the Monkhorst pack for 
phonon calculation but this time even the kpoints are the same as relaxation 
input.
Any help would be appreciated
ThanksZiba

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] strange force in phonon calculation

[Ziba Torkashvand]

Hello everyone,
I'm trying to do phonon calculation for some hexagonal structures.
Once I'm relaxing my structure up to 0.0004 eV/Ang after the first MD step
of phonon calculation without any displacement the maximum force will be
0.002 eV/Ang but still there is no negative frequency.
This time I've relaxed my structure up to 0.0002 eV/Ang but in the first
step I'm receiving 0.015 eV/Ang which is leading to the negative
frequencies.
In the successful phonon calculations I just lowered the number of kpoint
in the Monkhorst pack for phonon calculation but this time even the kpoints
are the same as relaxation input.
Any help would be appreciated

Thanks
Ziba

[image: Mailtrack]

Sender
notified by Mailtrack

09/05/21,
12:12:08 PM

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)