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Assignment 1

Create a python script that converts Hartree units to the units given in the table

Assignment 2

Create a script that asks for an integer number and then prints information about that number:

  • Is the integer odd or not.
  • Is the integer devisable by 3.
  • Is the integer devisable by 4.
  • Is the integer devisable by 5.

Assignment 3

Improve the car game to give more adequate responses to commands. For example, if the car has been already started, the script should reply to the user that the car is already running.

Hint: Use an additional variable to store the current state of the car.

Assignment 4

Create a script that computes the mean value of a list of integer numbers. Don't use the built-in sum function.

Assignment 5

Define a string variable that contains a meaningful text (having multiple words and sentences). Then print the text in a reverse order, i.e. the order of the words is reversed.

Hint: See str methods split and join.

Assignment 6

Create a script that iterates through a list of strings and removes all entries that are anagrams of previous entries. Example:

["abc", "def", "ghi", "cba", "bac", "fed"] -> ["abc", "def"]

Hint: Use sort to detect duplicates.

Assignment 7

Go through and refactor all homework and classwork script files so far such that the code is extracted into meaningful functions where applicable.

Assignment 8

Take any Gaussian output file. Write a python script that reads the file and extracts (with regex) the dipole moment of the molecule.

Hint: Detect the last line Dipole moment (field-independent basis, Debye):. Then from the next line get the values of the three components.

Assignment 9

Similar to the previous, extract the quadrupole moment form a Gaussian output file. If not done already, try to read the file line by line rather than loading the entire content at once.

Assignment 10

Generate Gaussian input files from the given file for each basis set from the list basis_sets = {"STO-3G", "3-21G", "6-21G", "4-31G", "6-31G", "6-31G", "6-311G"}. The generated files should have a file extension txt. Using the module pathlib, list all files with txt suffix (see the glob method) and change the suffix to gjf (see methods with_suffix and rename)

Assignment 11

Complete the script and find the angle between the clock arms at a given hour. Check the solution by adding and running the test.

Assignment 12

Use Python with the queue system on node1 (62.44.108.40) while acquainting yourself with the modules os and sys.

As an alternative to the bash script that is used for running Guassian jobs, complete the python script to compute and print the first N Fibonacci numbers with the help of a for loop.

Explanation: The os module provides functionality for accessing environment variables through a dictionary called environ and for changing the working directory. The sys module allows access to command line arguments, e.g.:

python script.py arg1 arg2 arg3

In the above case the list sys.argv will have 4 entries. The first entry is always the name of the script that is being run followed by command line arguments.

Here the if __name__ == '__main__': construction is used to isolate code that is supposed to be executed only directly. That is, if the file is imported as a module this code will be skipped.

Hint: The Python3 version on the nodes is a bit old so you may have to change some parts of the code. For example, if you encounter a problem with the formatted string, use the format method of str as an alternative.

When you log into node1 and submit the script on the queue like this:

qsub -F "10" script.py

(-F forwards arguments to the script) you should get an output like this:

0
1
1
2
3
5
8
13
21

Assignment 13

Write a script that from a set of keywords for hybrid functionals: {B3LYP, B3P86, O3LYP} and a simple Gaussian input :

# HYB_FUNC/6-31G(d)

water energy

0   1
O  -0.464   0.177   0.0
H  -0.464   1.137   0.0
H   0.441  -0.143   0.0

generates input files and bash scripts

#!/bin/bash
#PBS -N INPUT_NAME
#PBS -lnodes=1:ppn=8:RAM32GB,walltime=1440:00:00
#PBS_O_WORKDIR=`pwd`
 export PBS_O_WORKDIR
 cd $PBS_O_WORKDIR

echo ================== hostfile ========================
cat  $PBS_NODEFILE
echo ============== end hostfile ========================

g16 INPUT_NAME.gjf

rm /storage/users/${USER}/G*

The python script must submit those bash scripts to the queue. That can be done with the help of the os module:

os.popen("qsub my_bash_script.sh")

Explanation: Why do we want to submit a bash script instead of a python script as we do in the previous exercise? That's because not all nodes have Python installed so by tweaking the parameters #PBS -lnodes=1:ppn=8:RAM32GB,walltime=1440:00:00 we might end up on a node that will return an error.