INSTRUCTIONS FOR DAY 1, EXERCISE 3

In this exercise, we will use PWSCF to obtain the equilibrium structure of a molecule.


Enter the directory ex3. You will see the following files:

Self-consistent (scf) calculations for Acetylene

Run the scf calculation:

    pw.x <  acetylene.scf.in >  acetylene.scf.out
xcrysden --pwo  acetylene.scf.out

Geometry Optimisation

&IONS 
ion_dynamics      = 'bfgs', 
pot_extrapolation = 'second_order', 
wfc_extrapolation = 'second_order', 
upscale           = 100, 
/ 
pw.x < acetylene.bfgs.in > acetylene.bfgs.out
grep ^! acetylene.bfgs.out | nl 
grep 'Total force' acetylene.bfgs.out | nl

Optional things if you have time

Keeping atoms fixed

Look at the coordiantes in the input file

ATOMIC_POSITIONS bohr 
    C      0.000000000    0.000000000    0.000000000    0  0  0 
    C      2.100000000    0.000000000    0.000000000    1  1  1 
    H     -1.600000000    0.400000000    0.000000000    1  1  1 
    H      3.600000000   -0.400000000    0.000000000    1  1  1 

The final three columns determin which atoms are fixed. In the above case the first atoms has its x,y and z coordinates fixed (more precisely pwscf will multiply the forces on atom one by the numbers in the last three columns - so in this case set them to zero).
Perform a constrained calculation - allowing only the H atoms to move