[ase-users] ase-users Digest, Vol 107, Issue 11

[Heine Hansen]

Dear Yu-Ren Chen,

You should use the indices keyword of the ase.vibrations class to
control the size of the hessian.
Please see https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html

Best Regards,
Heine Hansen


On Wed, May 10, 2017 at 11:00 AM,
<ase-users-request at listserv.fysik.dtu.dk> wrote:

> Message: 3
> Date: Wed, 10 May 2017 08:00:19 +0000
> From: ??? <b00504051 at ntu.edu.tw>
> To: "ase-users at listserv.fysik.dtu.dk"
>         <ase-users at listserv.fysik.dtu.dk>
> Subject: [ase-users] Atoms' Constraints
> Message-ID:
>         <E689EE675085A04195F34C46063173F302C5F323EA at MBox2-2.ntu.internal>
> Content-Type: text/plain; charset="big5"
>
> Dear ASE users,
>
> I am using ase.io.read() to read in following POSCAR in VASP format to do a normal mode analysis:
>
> ---
>
> H O
>    1.00000000000000
>     10.0000000000000000    0.0000000000000000    0.0000000000000000
>      0.0000000000000000   10.0000000000000000    0.0000000000000000
>      0.0000000000000000    0.0000000000000000   10.0000000000000000
>    H    O
>      2     1
> Selective dynamics
> Cartesian
>         5.1707077079      4.0137770615      5.2080185115   F   F   F
>         5.0954999575      5.5514905157      5.1493322874   T   T   T
>         5.5902191105      4.8193934419      5.5566036301   T   T   T
>
>   0.00000000E+00  0.00000000E+00  0.00000000E+00
>   0.00000000E+00  0.00000000E+00  0.00000000E+00
>   0.00000000E+00  0.00000000E+00  0.00000000E+00
>
> ---
>
> Although it does not make too much sense here, I have fixed one of the H atoms hoping to obtain the eigenvalues of a partial Hessian instead of the full Hessian. After using the ase.io.read function, it shows: ('atoms:', Atoms(symbols='H2O', pbc=True, cell=[10.0, 10.0, 10.0], constraint=FixAtoms(indices=[0]))). If I understand this correctly, ASE has recognized that the first atom should be fixed. However, when I run the vibrational calculation using vib.run() and vib.summary(), it shows the following.
>
> ---
>
> ---------------------
>   #    meV     cm^-1
> ---------------------
>   0  136.1i   1097.5i
>   1   61.2i    493.9i
>   2   37.2i    299.6i
>   3   24.1i    194.1i
>   4    3.9      31.2
>   5   27.6     222.6
>   6  156.8    1264.8
>   7  172.2    1389.0
>   8  447.4    3608.8
> ---------------------
> Zero-point energy: 0.404 eV
>
> ---
> There is a problem that I cannot figure out. Since I fix one H atom, I expect that it should only show 6 values, but it gives me 9 values. In other words, the degrees of freedom of the first atoms has not been fixed. In line with that, the POSCAR files generated by ASE do feature structures that have the first atom moved from the initial position. Can anyone help me with fixing the atoms for the normal mode analysis?
>
> Yu-Ren Chen
> Institute of Atomic and Molecular Sciences, Academia Sinica
>
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