Laura at 02:52, 15 August 2025

2025-08-15T02:52:10Z

Laura at 22:14, 22 July 2025

2025-07-22T22:14:13Z

Laura: Created page for python script that plots potenital energy surfaces

2025-07-22T05:10:15Z

Created page for python script that plots potenital energy surfaces

New page

=Extracting Scan Data From GaussView=
Currently this script requires you first extract the data from your scans from GaussView.
For each calculation making up your overall scan:
* In GaussView open your .log file
* Go to Results then Scan to open the Gaussian formatted PES
* Right click on the plot and select Save Data...
* Save your data as a .txt file

=Running plot_PES.py=
This script is broken into 2 files. The first is a customisation file that you can edit to change the title, x axis label, plot colour, and save location of the produced figure. You can find a list of colours and their names here: [https://matplotlib.org/stable/gallery/color/named_colors.html colours]

* Copy the below code into a script called "PES_custom.py"
<pre>
x_label = "Dihedral Angle"
plot_title = "Potenital Energy Scan over Rotation of Imidazolium Ethyl Group"
plot_colour = "black"
centre_on_zero = True
save_fig = False
fig_filename = "test_save.png"
</pre>

The second file is the main script you will call. This needs to be in the same place as the customisation file you just created.

* Copy the below code into a script called "plot_PES.py"
* To execute type: python plot_PES.py scan_type input_filename_1 input_filename_2
* Depending on your customisation file, this will either display a figure with your PES plot or save the plot under the file name you gave in PES_custom.py

IMPORTANT NOTES:
* Replace scan_type with the type of scan that you did (e.g bond_angle, bond_length, dihedral_angle)
* Your input files .txt files you saved from Gaussian
* You can list as many input files as you need, just please omit the file extensions
* You can choose whether or not to save your figure as a .png automatically by setting save_fig = True in PES_custom.py
* If you do not automatically save your figure, the script will only stop running when you close the figure
* Any issues flick me an email at laura.doyle@vuw.ac.nz :)

<pre>
import sys
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import PES_custom as pes

dir = os.getcwd()

supported_scans = ['bond_length', 'bond_angle', 'dihedral_angle']

if len(sys.argv) < 3:
print("To run the script please type: python PES_plotter.py scan_type input_file_name_1 input_file_name_2",
" \( and so on for as many .txt files as you have)")
sys.exit()

else:
if str(sys.argv[1]) not in supported_scans:
print("WARNING: This scan type may not be supported, please double check results.",
" Supported scan types are:", *supported_scans, sep="\n")

data_files = []
for i in range(len(sys.argv)-2):
data_files.append(str(sys.argv[i+2])+'.txt')

scan_type = sys.argv[1]

def center_angles(angle):
# Adjust scan angles to be between -180 and 180 degrees
centered = ((angle + 180) % 360) - 180
return centered

# Grab the data from the scan data files and combine into a single dataframe
PES_data = pd.DataFrame()
for data_file in data_files:
df = pd.read_csv(data_file,sep='\s+',skiprows=4,names=["Angle", "Energy"])
PES_data = pd.concat([PES_data, df], ignore_index=True)

# If True, adjusts the scan angles to be centered about 0
if pes.centre_on_zero and "angle" in scan_type: PES_data["Angle"] = PES_data["Angle"].apply(center_angles)

# Sorts the data by scanning variable
sorted_PES_data = PES_data.sort_values(by="Angle")

# Converts Energy from a.u. to kJ/mol and zeroes the energy to the minimum
energies_kj = sorted_PES_data["Energy"] * 2625
zeroed_energies_kj = energies_kj - np.min(energies_kj)

# Plots the potential energy surface
ax = plt.axes()
ax.plot(sorted_PES_data["Angle"], zeroed_energies_kj, c=pes.plot_colour, marker="o", linewidth=0.75)
ax.set_xlabel(pes.x_label)
ax.set_ylabel("Energy (kJ/mol)")
ax.set_title(pes.plot_title)

if pes.save_fig:
plt.savefig(pes.fig_filename)
else: plt.show()

sys.exit()
</pre>

@@ Line 1: / Line 1: @@
 =Extracting Scan Data From GaussView=
@@ Line 13: / Line 15: @@
 * Copy the below code into a script called "PES_custom.py"
 <pre>
-x_label = "Dihedral Angle"
+x_label = "Dihedral Angle (degrees)"
 plot_title = "Potenital Energy Scan over Rotation of Imidazolium Ethyl Group"
 plot_colour = "black"
@@ Line 90: / Line 92: @@
 ax.plot(sorted_PES_data["Angle"], zeroed_energies_kj, c=pes.plot_colour, marker="o", linewidth=0.75)
 ax.set_xlabel(pes.x_label)
-ax.set_ylabel("Energy (kJ/mol)")
+ax.set_ylabel("Relative Energy (kJ/mol)")
 ax.set_title(pes.plot_title)

Mod:Hunt Research Group/plot potenital energy surface - Revision history

Laura at 02:52, 15 August 2025

Laura at 22:14, 22 July 2025

Laura: Created page for python script that plots potenital energy surfaces