ACSE 9 Independent Research Project

Author: Devang Patel

Supervisors:

• Prof. Dominik Weiss (Imperial College London, UK)
• Dr. James Percival (Imperial College London, UK)
• Prof. Patricia Hunt (Victoria University of Wellington, NZ)

This code was written for my ACSE MSc research project from 1st June - 27th August 2021. It calculates the reduced partition function ratio between 2 singly substituted isotopologues by extracting their vibrational frequencies from Gaussian log files.

Layout

Modules

calculations - module that contains functions to calculate the reduced partition function ratio

extractions - module that contains functions that extract frequencies, temperature and isotopic information from a Gaussian log file

file_io - module for checking file existence and inspecting files

isotope_contribution - module that contains functions to ascertain isotope vibrations for frequencies, and a csv file atomic_number.csv used as a lookup table for atomic numbers of elements,

Folders

input_files - folder to store input files

output_files - folder to store output files

tests - contains log files, command line outputs, and an excel spreadsheet calculations.xlsx used in testing extraction, calculation + script.py functionality.

Files

environment.yml - depedency installation file for Anaconda

requirements.txt - dependency installation file for Pip

Scripts

scripts.py - Main script for calculation of the reduced partition function. See below for usage instructions.

tests.py - Script to run extraction and calculation tests with ZnCl4 and ZnH2O log files.

Installation / Usage Instructions

To download the code, either download as a .zip file, or if you have Git installed, run:

git clone https://github.com/endevor-music/rpfr_calculator.git

To be on the safe side, ensure you are in the root directory before creating/activating a virtual environment.

Windows

Pip

To create and activate the virtual environment (venv) and install the required packages WITHIN the root directory, run:

python -m venv venv 
# if using Command Prompt:
venv\Scripts\activate.bat
# if using Windows Powershell
venv\Scripts\activate.ps1
pip install -r requirements.txt

To deactivate, run:

venv\Scripts\deactivate.bat

Anaconda - https://www.anaconda.com/

Once Anaconda is installed, ensure the Anaconda Prompt terminal, indicated by (base) is running.

To create a virtual environment, install the required packages and activate the environment run:

conda env create --name venv --file environment.yml
conda activate venv

To deactivate run

conda deactivate

Linux - Ubuntu

Pip

Installing Pip and the venv module:

$ sudo apt install python3-pip
$ sudo apt install python3.8-venv

Installing and activating the virtual environment:

$ python3 -m venv venv
$ source venv/bin/activate
$ pip install -r requirements.txt

Deactivating the virtual environment:

$ deactivate

Running the script

To run the python script, run

(venv) python script.py arg1 arg2 arg3 arg4 arg5

with the argument list as follows:

• arg1 - path to light isotopic log file e.g. ./tests/log_files/zinc/ZNCL4_B_64.log
• arg2 - path to heavy isotopic log file e.g. ./tests/log_files/zinc/ZNCL4_B_66.log
• arg3
  • y if the molecule is linear
  • n if the molecule in non-linear
• arg4 - path to output file e.g. ./output_files/file.txt - can be anything the user wishes
• arg5 - print variable
  • False: prints out just basic information (input filenames, temperature, reduced partition function ratio)
  • True: prints out basic info + extra information (item convergence table, low frequencies)

For example, running the following:

python script.py tests/log_files/zinc/ZNCL4_B_64.LOG tests/log_files/zinc/ZNCL4_B_66.LOG n ./output_files/file.txt True

would run the program on the input files (tests/log_files/zinc/ZNCL4_B_64.LOG and tests/log_files/zinc/ZNCL4_B_66.LOG), and calculate the expected frequencies given the molecule is non-linear (due to n), and output all extracted data (True) to the output file ./output_files/file.txt.

Running tests

To run basic tests, simply run tests.py. Currently the test functions for extractions and calculations are run using the ZnCl4 ans ZnH2O log files in ./tests/test_files.

A collection of files to view the functionality of script.py with respect to the presence/absence of temperature, isotopic information and frequencies in log files is available to view in tests\log_files\water\.

To save the command line output of the tests to a file to view at a later time (e.g. tests\log_files\water\frequency\outputs\H2O_both_freq_cmd.txt), run:

python script.py <argument list> > <path_to_file>

Licensing

MIT License