Dear Andrei and Marcos,
1) As a DFT problem, i used La in its +3 state along with non-linear core
correction with pseudocore, Not semocore
states.
La(+3) PP gen configuration is :
5s2 1.83
5p6 2.19
5d0 3.00
4f0 1.25 with pseudocore radius 1.50 bohr.
I think i need to change pseudocore ? Please give suggestions over this
why i should increase or decrease the
pseudocore? how it can affect the frequencies?
2) I used FC Displ= 0.005Bohr, hopefully within harmonic approximation.
3) I Relaxed the system with MaxForceTol= 0.0001 ev/Ang.
4) Can SIESTA calculates bulk modulus directly? I have not seen any flag
which calculates bulk modulus.
or do i need to calculate it through fitting process using Murnaghan
equation of state?
with Regards,
1009u
2009/12/12 Marcos Veríssimo Alves <[email protected]>
> Sonu,
>
> What Andrei refers to by displacement amplitude is not the eggbox effect,
> it's the displacement applied by siesta to a given atom when you do the
> phonon run. As you may know, siesta calculates the force constant matrix by
> applying a displacement plus or minus delta to a given atom on each of the
> cartesian directions. Sometimes, siesta's default displacement can be too
> large because of the anharmonicities he mentioned, and then you'll get wrong
> results. So one thing you can do is to check which flga controls the
> amplitude of atomic displacements for a phonon calculation, make it smaler,
> re-run your phonon calculation and see if anything changes in your results.
>
> Another thing to be careful about is the degree of relaxation of your
> system, even though I'm not so sure it would be a major source of error for
> you. You are calculating forces on other atoms due to the displacement on a
> pretty small distance scale, so on the relaxation of your system prior to
> the force constant matrix calculation, you should have the force tolerance
> set to a very small value, much smaller than the default 0.04 eV/Ang. 0.001
> would be better already, although depending on your availability of time and
> patience, you could set it to even lower values :)
>
> Cheers,
>
> Marcos
>
>
> On Sat, Dec 12, 2009 at 6:06 PM, sonu kumar <[email protected]> wrote:
>
>> Dear Sir,
>>
>> Effect of displacement amplitude i suppose is eggbox effect. I have not
>> checked it, will CHECK it out, although for reasonable values of
>> meshcutoff, the effect of eggbox on the total energy or on the relaxed
>> structure is normally unimportant as has been written in SIESTA manual.
>>
>> Sorry, right now information of La(+3) PP is not with me.
>>
>> Also,now, i will do rest of the calculations as have been asked by you.
>>
>> Thank you very much
>>
>> 1009u
>>
>>
>>
>>
>> On Sat, Dec 12, 2009 at 8:58 PM, <[email protected]> wrote:
>>
>>> Dear 1009u,
>>>
>>> the things to look at are:
>>> 1. Your acoustic modes are close enough to zero, that means that,
>>> most probably, an insufficient MeshCutoff is not your problem.
>>> 2. The frequencies which are supposed to be degenerate are reasonably
>>> close, that means that numerical errors due to k-mesh etc.,
>>> are not obviously to blame.
>>> 3. You say that not all frequencies are bad from which I conclude
>>> that the rest (out of 7, or so? I do not have the symmetry decomposition
>>> at hand) modes, are OK. This is not bad.
>>> For the modes which worry you, you should have a more attentive look at
>>> - the effect of the displacement magnitude; some modes are strongly
>>> anharmonic and depend on it.
>>>
>>> If the difference persists, it can be either
>>> - the general DFT problem (do you have other calculations to compare?),
>>> or
>>> - the experiment problem (are the data reliable? Are other experiments
>>> available? Do these frequencies strongly depend on temperature?).
>>>
>>> After eliminating all these source of difference, whatever rests is
>>> a purely Siesta problem - pseudos and bases. It does not mean, though,
>>> that you can tune it easily. How good is your La ? Semicores etc.
>>>
>>> Do the elastic properties come out right? To test them might be
>>> not so easy for a hexagonal structure. Take a simple cubic compound
>>> with your La and check the bulk modulus. Compare it against WIEN2k
>>> or other all-electron calculation.
>>>
>>> Good luck
>>>
>>> Andrei Postnikov
>>>
>>>
>>> > Thank you Sir,
>>> >
>>> > I have done few calculations of zone center phonons using primitive
>>> unit.
>>> >
>>> > But i got wrong zone center phonon frequencies ( not all ) in LaB6
>>> system.
>>> > Similarly in carbide systems.
>>> >
>>> > e.g. For LaB6 system
>>> >
>>> > Expt. freq
>>> > Freq (by SIESTA)
>>> >
>>> > F1u mode ( translation) 210
>>> > 181.12,182.30, 182.97
>>> >
>>> > F1u mode (bending) 1095
>>> > 877.12, 877.60, 879.85
>>> >
>>> >
>>> > and also
>>> >
>>> > Accoustical
>>> > modes
>>> 0.0310,
>>> > 0.0396, 0.0766,
>>> >
>>> >
>>> > Many times i changed the meshcutoff (kept more than 400 Ryd) and kgrid
>>> (
>>> > kept more than 25 Bohr) to get the required frequiences, But only the
>>> > digits after decimal place changes i.e meshcutoff and kgrid doesn't
>>> > change
>>> > the frequencies appreciably.
>>> >
>>> > Is the problem because of Pseudo-potential and basis.?
>>> >
>>> > I also checked the frequencies using GGA approximation to particle
>>> density
>>> > functional, but no success?
>>> >
>>> > hope that the information given is sufficient.
>>> >
>>> > With Regards
>>> >
>>> > 1009u
>>> >
>>> >
>>> >
>>>
>>>
>>
>>
>> --
>> 1009U
>>
>
>
--
1009U
