[gpaw-users] normal mode calculation via ase

[Jens Jørgen Mortensen]

On 7/5/19 11:50 AM, Jay Wai via gpaw-users wrote:
> Dear users,
> 
> I am trying to calculate the free energy of a h2o gas molecule, but I am 
> stuck in the step of normal mode calculation because of imaginary 
> frequencies.
> 
> My code is as follows:
> 
> calch2o = GPAW(mode=PW(800), xc='PBE', kpts={'size': [3,3,1]}, 
> symmetry='off', convergence={'energy':0.0001, 'density':1e-6}, 
> basis='dzp', txt='h2o.txt')
> h2o = molecule('H2O')
> h2o.set_cell([15,15,15])
> h2o.set_pbc([1,1,1])
> h2o.center()
> h2o.set_calculator(calch2o)
> opth2o = BFGS(h2o, trajectory='h2o.traj')
> opth2o.run(fmax=0.02)
> vibh2o = Vibrations(h2o)
> vibh2o.run()
> 
> I have run a similar code for other molecules, including co, h2, co2 and 
> found that imagnary frequencies disappear for those molecules as I 
> increased the cut-off energy and the number of kpts.
> That's why I set the cut-off energy to be so high (800) and included 
> several k-points for a single molecule calculation.

More than 1 k-point should not help for a molecule.

> The result of normal mode analysis is as follows:
> ---------------------
>    #    meV     cm^-1
> ---------------------
>    0    7.8i     63.3i
>    1    7.1i     57.0i
>    2    1.8      14.2
>    3    3.1      25.3
>    4    5.2      41.6
>    5    7.8      63.0
>    6  197.4    1592.5
>    7  460.8    3716.8
>    8  473.4    3817.9
> ---------------------
> 
> My quesiton is how I can change my code not to get imaginary frequencies.
> I've tried the followings, but none of them worked.
> a) set nfree to be 4 when calling Vibrations()
> b) set energy convergence criteria to be 1E-6
> c) try other cut-off energies: 400, 500, 600
> d) set fmax to be smaller values in geometry optimization
> 
> Can anybody help me on this?
> 
> Or, can I just use the last three frequencies and call 
> ase.IdealgasThermo function because we know that h2o only have three 
> normal modes of vibration?

You can also play with delta<0.01:

 
https://wiki.fysik.dtu.dk/ase/dev/ase/vibrations/modes.html#ase.vibrations.Vibrations

but I would just use the three last modes.

Jens Jørgen

> 
> Thank you,
> 
> Jay
> 
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