[ase-users] Atoms' Constraints

[陳佑任]

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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