3. Qmflows and Nano-qmflows workflows
- The single_points workflow
- The absorption_spectrum workflow
- The distribute_derivative_couplings workflow
In your working directory, copy the folder containing all the files you will need for this tutorial:
cp -r /projects/academic/cyberwksp21/Instructors_material/jzito/nano-qmflows/ .
Please refer to the nano-qmflows’s documentation to complete the following assignments.
1. The single_points workflow
A single point calculation on the relaxed geometry of a Cd33Se33 system has been performed according to
the Single points calculation’s tutorial
(see the corresponding input file in your
Use the provided
Cd33Se33.hdf5 file to:
- Calculate the HOMO-LUMO gap in eV.
- Plot the energy (in eV) of the Kohn-Sham orbitals considered in the active space. (Suggestion: use matplotlib.pyplot.barh)
2. The absorption_spectrum workflow
Calculate the oscillator strength of the lowest lying excited states of our Cd33Se33 system within the single orbital transitions approximation.
To do that, edit the input file
absorption_spectrum_Cd33Se33.yml provided in the directory
2_absorption_spectrum according to the previous requirements (consult the tutorial
Absorption Spectrum), then
submit your calculation using the
launch.sh submission script. Use the provided
Once the calculation is completed, copy locally the result file
output_0_sing_orb.txt from your
scratch directory and interpret it using
the last part of the tutorial.
- How many singly excited configurations do you expect to find there?
- What is the energy of the first excited state within the single orbital approximation? Is this result in line with the previous exercise?
- Plot the absorption spectrum for the Cd33Se33 system in the energy interval 0-2 eV using a sigma value of 0.1. (Suggestion: Import the
from nanoqm.analysis import convoluteand have a look at the script
3. The distribute_derivative_couplings workflow
In the directory
3_derivative_couplings, you will find the input
distribute_derivative_couplings_Cd33Se33.yml that has been used to distribute the
last twenty points of a ground state molecular dynamics trajectory for the Cd33Se33
Cd33Se33_MD_last20.xyz) into four chunks. For each chunk, the values of the
overlaps and couplings have been calculated and stored, respectively, in
Follow the Derivative Couplings tutorial to merge these files into a unique
chunk_0123.hdf5 file and calculate the overlaps and couplings amongst the missing pairs of points.
- How many couplings are missing and need to be calculated? How many couplings would you expect to find in the final updated
- Use the updated
chunk_0123.hdf5to plot the dependence of the energy (in eV) of the LUMO and LUMO+1 over time.
- Use the updated
chunk_0123.hdf5to the retrieve the LUMO-LUMO+1 overlaps and couplings and plot their value in time.