Overview

Teaching: min
Exercises: min

Questions

Objectives

Tutorial

1. Setup
2. The single_points workflow
3. The absorption_spectrum workflow
4. The distribute_derivative_couplings workflow

0. Setup

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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

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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 1_single_points directory).

Use the provided Cd33Se33.hdf5 file to:

1. Calculate the HOMO-LUMO gap in eV.
2. 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

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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 Cd33Se33.hdf5 file.

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.

1. How many singly excited configurations do you expect to find there?
2. What is the energy of the first excited state within the single orbital approximation? Is this result in line with the previous exercise?
3. 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 convolute function with from nanoqm.analysis import convolute and have a look at the script convolution.py)

3. The distribute_derivative_couplings workflow

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In the directory 3_derivative_couplings, you will find the input file 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 system (Cd33Se33_MD_last20.xyz) into four chunks. For each chunk, the values of the overlaps and couplings have been calculated and stored, respectively, in the files chunk_0.hdf5, chunk_1.hdf5, chunk_2.hdf5 and chunk_3.hdf5. 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.

1. How many couplings are missing and need to be calculated? How many couplings would you expect to find in the final updated chunk_0123.hdf5?
2. Use the updated chunk_0123.hdf5 to plot the dependence of the energy (in eV) of the LUMO and LUMO+1 over time.
3. Use the updated chunk_0123.hdf5 to the retrieve the LUMO-LUMO+1 overlaps and couplings and plot their value in time.

Key Points