2.2 Preparing Qbox Input Files from the XYZ file with Displaced Coordinates
In the last step, we stored normal-mode displaced coordinates into a file named enmfd_phonon.xyz. Just like example 1.2, here we have to convert xyz file into single/multiple qbox input file(s) using xyz2qbox tool.
While computing the phonon frequencies, we would also compute the EPCEs and ZPR. Therefore we need to compute band energies of a few valence and conduction bands. For that purpose we need to include virtual orbitals by specifying a non-zero nempty values. We would also require to save wavefunctions of HOMOs and LUMOs for each displaced coordinates, which can be done using qbox plot command.
For CO2, HOMO is 2-fold degenerate and their orbital/band indices are 7 and 8, while LUMO is singly degenerate with band index 9.
[1]:
%run ../../../utils/qbox_utils/xyz2qbox.py enmfd_phonon.xyz
File enmfd_phonon.xyz has 3 number of atoms in each frame and a total 19 number of frames.
No of species: 2
Present species are:
O_species
C_species
The file enmfd_phonon.xyz is an i-PI output with pos_unit: angstrom and cell_unit: angstrom
Enter start frame number: (Default = 1)
Enter last frame number: (Default = 19)
Enter step frame: (Default = 1)
Enter qbox command for 1st iteration: (Default = ' randomize_wf, run -atomic_density 0 100 10')
Hint: more than one commands should be separated by a comma.
Enter qbox run command: (Default = ' run 0 60 10')
Hint: more than one commands should be separated by a comma.
Enter qbox plot command: (Default = ' None')
Hints:
(1) Example: plot options filename (without .cube extension)
(2) More than one commands should be separated by a comma.
plot -wf 7 wf7, plot -wf 8 wf8, plot -wf 9 wf9
Enter qbox spectrum command: (Default = ' None')
Hints:
(1) Example: spectrum options filename (without .dat extension)
Do you want to save sample for each configurations (y/n)? (Default = n)
Enter filename of qbox input: (Default = qbox.i) enmfd-1.i
Enter xc: (Default = PBE)B3LYP
Enter wf_dyn: (Default = JD)
Enter ecut (Ry): (Default = 50.0)
Enter scf_tol (Ry): (Default = 1e-08) 1e-12
Enter nempty: (Default = 100) 5
Enter nspin (1/2): (Default = 1)
Enter delta_spin: (Default = None)
Enter net_charge: (Default = 0)
Enter pseudopotential: (Default = ONCV_PBE-1.0)
Warning!
Files:
O_ONCV_PBE-1.0.xml
C_ONCV_PBE-1.0.xml
must be present in the following pseudo-potential directory.
../pseudos/
This created a qbox input file with name enmfd-1.i. Just like example 1.2, here also multiple input file can be (must for a large system) created. For that purpose the bash wrapper many_xyz2qbox.sh located at util/qbox_util folder can be used instead of running xyz2qbox.py multiple times. Let us have a look at the qbox input file enmfd-1.i. Before that let us restart the kernel to finish the file writing.
[1]:
%%bash
cat enmfd-1.i
set xc B3LYP
set wf_dyn JD
set ecut 50.00
set scf_tol 1.00e-12
species O_species ../pseudos/O_ONCV_PBE-1.0.xml
species C_species ../pseudos/C_ONCV_PBE-1.0.xml
# Frame 1/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
atom O1 O_species 0.000000 0.000000 2.186665
atom O2 O_species 0.000000 0.000000 -2.186662
atom C3 C_species 0.000000 0.000000 -0.000003
set nempty 5
randomize_wf
run -atomic_density 0 100 10
plot -wf 7 wf7_frame-1.cube
plot -wf 8 wf8_frame-1.cube
plot -wf 9 wf9_frame-1.cube
# Frame 2/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.000000 -0.000000 2.475340
move O2 to -0.000000 -0.000000 -1.897987
move C3 to -0.000000 -0.000000 0.288672
run 0 60 10
plot -wf 7 wf7_frame-2.cube
plot -wf 8 wf8_frame-2.cube
plot -wf 9 wf9_frame-2.cube
# Frame 3/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.000000 0.000000 1.897990
move O2 to 0.000000 0.000000 -2.475337
move C3 to 0.000000 0.000000 -0.288678
run 0 60 10
plot -wf 7 wf7_frame-3.cube
plot -wf 8 wf8_frame-3.cube
plot -wf 9 wf9_frame-3.cube
# Frame 4/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.000000 0.448620 2.186665
move O2 to -0.000001 -0.172131 -2.186662
move C3 to -0.000000 0.138244 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-4.cube
plot -wf 8 wf8_frame-4.cube
plot -wf 9 wf9_frame-4.cube
# Frame 5/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.000000 -0.448620 2.186665
move O2 to 0.000001 0.172131 -2.186662
move C3 to 0.000000 -0.138244 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-5.cube
plot -wf 8 wf8_frame-5.cube
plot -wf 9 wf9_frame-5.cube
# Frame 6/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.352008 -0.000001 2.186665
move O2 to -0.355089 0.000000 -2.186662
move C3 to -0.001542 -0.000000 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-6.cube
plot -wf 8 wf8_frame-6.cube
plot -wf 9 wf9_frame-6.cube
# Frame 7/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.352008 0.000001 2.186665
move O2 to 0.355089 -0.000000 -2.186662
move C3 to 0.001542 0.000000 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-7.cube
plot -wf 8 wf8_frame-7.cube
plot -wf 9 wf9_frame-7.cube
# Frame 8/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.290402 -0.000001 2.186665
move O2 to -0.286941 0.000001 -2.186662
move C3 to -0.288672 -0.000000 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-8.cube
plot -wf 8 wf8_frame-8.cube
plot -wf 9 wf9_frame-8.cube
# Frame 9/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.290402 0.000001 2.186665
move O2 to 0.286941 -0.000001 -2.186662
move C3 to 0.288672 0.000000 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-9.cube
plot -wf 8 wf8_frame-9.cube
plot -wf 9 wf9_frame-9.cube
# Frame 10/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.000000 -0.100021 2.186665
move O2 to 0.000000 -0.416340 -2.186662
move C3 to -0.000000 -0.258181 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-10.cube
plot -wf 8 wf8_frame-10.cube
plot -wf 9 wf9_frame-10.cube
# Frame 11/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.000000 0.100021 2.186665
move O2 to -0.000000 0.416340 -2.186662
move C3 to 0.000000 0.258181 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-11.cube
plot -wf 8 wf8_frame-11.cube
plot -wf 9 wf9_frame-11.cube
# Frame 12/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.031448 0.010314 2.186665
move O2 to 0.031448 0.010314 -2.186662
move C3 to -0.083784 -0.027478 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-12.cube
plot -wf 8 wf8_frame-12.cube
plot -wf 9 wf9_frame-12.cube
# Frame 13/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.031448 -0.010314 2.186665
move O2 to -0.031448 -0.010314 -2.186662
move C3 to 0.083784 0.027478 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-13.cube
plot -wf 8 wf8_frame-13.cube
plot -wf 9 wf9_frame-13.cube
# Frame 14/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.010314 -0.031448 2.186665
move O2 to 0.010314 -0.031448 -2.186662
move C3 to -0.027478 0.083784 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-14.cube
plot -wf 8 wf8_frame-14.cube
plot -wf 9 wf9_frame-14.cube
# Frame 15/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.010314 0.031448 2.186665
move O2 to -0.010314 0.031448 -2.186662
move C3 to 0.027478 -0.083784 -0.000003
run 0 60 10
plot -wf 7 wf7_frame-15.cube
plot -wf 8 wf8_frame-15.cube
plot -wf 9 wf9_frame-15.cube
# Frame 16/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.000000 0.000000 2.216857
move O2 to 0.000000 0.000000 -2.216853
move C3 to -0.000000 -0.000000 -0.000004
run 0 60 10
plot -wf 7 wf7_frame-16.cube
plot -wf 8 wf8_frame-16.cube
plot -wf 9 wf9_frame-16.cube
# Frame 17/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.000000 -0.000000 2.156473
move O2 to -0.000000 -0.000000 -2.156471
move C3 to 0.000000 0.000000 -0.000002
run 0 60 10
plot -wf 7 wf7_frame-17.cube
plot -wf 8 wf8_frame-17.cube
plot -wf 9 wf9_frame-17.cube
# Frame 18/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to -0.000000 0.000000 2.195700
move O2 to -0.000000 0.000000 -2.177627
move C3 to 0.000000 -0.000000 -0.024074
run 0 60 10
plot -wf 7 wf7_frame-18.cube
plot -wf 8 wf8_frame-18.cube
plot -wf 9 wf9_frame-18.cube
# Frame 19/19 from enmfd_phonon.xyz#
set cell 20.000000 0.000000 0.000000 0.000000 20.000000 0.000000 0.000000 0.000000 20.000000
move O1 to 0.000000 -0.000000 2.177630
move O2 to 0.000000 -0.000000 -2.195697
move C3 to -0.000000 0.000000 0.024068
run 0 60 10
plot -wf 7 wf7_frame-19.cube
plot -wf 8 wf8_frame-19.cube
plot -wf 9 wf9_frame-19.cube
The next step is to submit those jobs and wait until all calculations finished properly. Once the calculations are finished, the obox outputs must be post-processed to compute the dynamical matrix. This will be the topic of exercise 1.2.3.
[ ]: