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Practical example

In this example, transition state for the ammonia flipping is computed. All calculations discussed here were performed using the PBE functional, Brillouin zone sampling was restricted to the gamma point. This practical example can be completed in a few seconds on a standard desktop PC. The starting structure for IDM simulation should be a reasonable guess for the transition state. POSCAR with the initial guess for the ammonia flipping:

ammonia flipping
1.
6. 0. 0.
0. 7. 0.
0. 0. 8.
H N
3 1
cart
       -0.872954        0.000000       -0.504000
        0.000000        0.000000        1.008000
        0.872954        0.000000       -0.504000
        0.000000        0.000000        0.000000

As an input for the dimer method, direction of unstable mode (dimer axis) is needed. This can be obtained by performing vibrational analysis. The INCAR file should contain the following lines:

NSW = 1
Prec=Normal
IBRION=5                 ! perform vibrational analysis
NFREE=2                  ! select central differences algorithm
POTIM=0.02               ! step for the numerical differenciation 
NWRITE=3                 ! write down eigenvectors of dynamical matrix after division by SQRT(mass)

After completing the vibrational analysis, we look up the hardest imaginary mode (Eigenvectors after division by SQRT(mass)!) in the OUTCAR file:

 12 f/i=   23.224372 THz   145.923033 2PiTHz  774.681641 cm-1    96.048317 meV
             X         Y         Z           dx          dy          dz
      5.127046  0.000000  7.496000     0.000001    0.522103   -0.000009
      0.000000  0.000000  1.008000    -0.000006    0.530068    0.000000
      0.872954  0.000000  7.496000    -0.000005    0.522067   -0.000007
      0.000000  0.000000  0.000000     0.000001   -0.111442    0.000001

and use the last three columns to define the dimer axis in POSCAR:

ammonia flipping
1.
6. 0. 0.
0. 7. 0.
0. 0. 8.
H N
3 1
cart
       -0.872954        0.000000       -0.504000        ! coordinates for atom 1
        0.000000        0.000000        1.008000
        0.872954        0.000000       -0.504000
        0.000000        0.000000        0.000000        ! coordinates for atom N
       ! here we define trial unstable direction:
        0.000001    0.522103   -0.000009        ! components for atom 1
       -0.000006    0.530068    0.000000
       -0.000005    0.522067   -0.000007
        0.000001   -0.111442    0.000001        ! components for atom N

In order to perform IDM calculation, INCAR should contain the following lines:

NSW = 100           
Prec=Normal
IBRION=44           !  use the dimer method as optimization engine
EDIFFG=-0.03

With this setting, algorithm converges in just a few relaxation steps. Further vibrational analysis can be performed to prove that the relaxed structure is indeed a first order saddle point (one imaginary frequency).


next up previous contents index
Next: Advanced MD techniques. Up: Improved dimer method Previous: Initial dimer axis   Contents   Index
N.B. Requests for support are to be addressed to: vasp.materialphysik@univie.ac.at