Difference between revisions of "ORCA---Computational-Chemistry/C2/Creating-an-Input-File/English"

Revision as of 14:59, 29 September 2023

Title of the script: Creating an Input File

Author: Madhuri Ganapathi, Rani Parvathy, Raj Singh, Arup Sarkar.

Keywords: Avogadro, gedit text editor, auto optimization, water molecule, bond length, bond angle, xyz file format, inp file format, spin multiplicity, video tutorial.

Visual Cue	Narration
Slide Number 1 Title slide	Welcome to this Spoken tutorial on Creating an Input File.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Create a 3D model of a molecule in Avogadro Optimize its geometry in Avogadro Measure the bond length and bond angle of the optimized molecule
Slide Number 3 Learning Objectives	Save the structure in XYZ file format in a folder Generate Orca input file using Extensions menu
Slide Number 4 System Requirements	To record this tutorial, I am using; Ubuntu Linux OS version 20.04 Avogadro version 1.2.0 Gedit Text Editor v3.36.2
Slide Number 5 Pre-requisites https://spoken-tutorial.org/tutorial-search/?search_foss=Avogadro&search_language=English	To follow this tutorial, learners should be familiar with Avogadro software. Please use the link below to access the tutorials on Avogadro.
Slide Number 6 ORCA Input File	Now we will create an input file for ORCA. ORCA accepts the input in the form of coordinates in xyz format. The input file in xyz format can be created using Avogadro or online servers. You can use any other software such as Jmol to create the input file.
Slide Number 7 ORCA Input File	Information on how to create an xyz file using online servers is provided in the Additional reading material.
Only Narration	Let us now open the Avogadro application.
Click the Show Applications icon located at the bottom left corner. In the search bar that appears type, Avogadro.	Click on the Show Applications icon located at the bottom left corner. In the search bar that appears type, Avogadro.
Click the Avogadro icon to open the application. In the Search bar next to the Start icon type Avogadro. Select Avogadro from the shown list.	Click the displayed Avogadro icon to open the application. Windows users can open Avogadro using the Start menu icon.
Cursor on the Panel.	Now we will create a 3D model of a water molecule.
Point to the Pencil tool. Click the Draw Tool icon on the toolbar.	Click the Draw Tool icon on the toolbar.
Point to Draw Settings. Point to Adjust Hydrogens check box.	Under the Draw Settings menu, Carbon is selected as the default Element. By default, the Adjust Hydrogens checkbox is checked for me. Check the Adjust Hydrogens checkbox if it is not checked for you.
Click the Element drop-down and select Oxygen.	Click on the Element drop-down and select Oxygen.
Click in the panel. Point to the water molecule in the panel.	Click in the panel. A 3D model of a water molecule is displayed on the panel.
Click on the Navigation tool and rotate the molecule.	Let us rotate and zoom the water molecule to see it clearly.
Cursor on water molecule.	Now we will optimize the geometry of the water molecule. Optimisation takes the molecule to a stable geometric structure.
Point to the symbol of Auto optimisation icon(E). Click the Auto Optimization Tool on the toolbar. Point to the Auto Optimization Settings menu.	Click the Auto Optimization Tool on the toolbar. The Auto Optimization Settings menu opens in the left panel.
Select MMFF94 as the Force Field. Point to MMFF94. Point to the Start button in the Auto Optimization Settings menu. Click the Start button.	From the Force Field drop-down select the MMFF94 option. Here MMFF94 is a Molecular Mechanics tool to minimize the energy. I will leave the default values as such and click the Start button.
Point to the molecule in the panel. In the panel, we see dE =0. Click the Stop button. Point to the auto-optimized molecule.	In the panel, if you see dE=0 the optimization process is completed. Click the Stop button after the molecule is optimized. Observe that if we click on Stop, the button switches to Start. Here the Start/Stop button is a toggle button. The water molecule is now auto-optimized.
Cursor on water molecule. Point to the symbol of the Click to Measure tool on the toolbar. Click the Click to Measure tool on the toolbar. Click on hydrogen and oxygen atoms.	Now let us measure the bond length of oxygen, hydrogen single bonds. Click the Click to Measure tool on the toolbar. Click on hydrogen and oxygen atoms.
Point to the bond length of oxygen and hydrogen bond.	The bond length is displayed at the bottom of the panel as 0.969 Å ( Angstroms) Let us note this value.
Click on the second hydrogen atom Point to the bond angle hydrogen, oxygen and hydrogen.	To measure the bond angle click on the second hydrogen atom. The bond angle is displayed as 104.0⁰ degrees. Let us again note this value.
Cursor on the interface.	Now let us save the file in XYZ file format.
Click the File menu >> select Save As option. Point to the dialog box. Point to the Home folder.	Click the File menu and select Save As option. Save Molecule As dialog box opens. We will save the water molecule in a new folder in the Home directory. You can choose your convenient location to save the file.
Point to the dialog box. Click the Create New Folder icon with a green plus mark. This icon is available in the top right corner of the dialog box.	In the dialog box click the Create New Folder icon with a green plus mark.
Point to the folder in the box. Type the name as water and press Enter key. Double-click the folder to open it.	A new folder appears in the dialog box. Type the name of the folder as water and press Enter. Then double-click the water folder to open it.
In the File name field, type filename as water.xyz Point to XYZ file format. In the Files of type, drop-down select XYZ file format. Click the Save button.	In the Filename field type the filename as water.xyz. In the Files of type, drop-down select XYZ file format. Click the Save button in the dialog box.
Click on the Files icon. Point to water folder in the Home directory.	Let us now go to the Home directory. Here we see the water folder in the Home directory.
Double click to open the water folder. Point to water.xyz file.	Open the water folder by double-clicking on it. It contains the water.xyz file. water.xyz file can be opened and modified using gedit text editor.
Right-click on the water.xyz file >> select Open With Text Editor.	Right-click on water.xyz file. Select the option Open With Text Editor. File opens in the text editor.
Point to 3. Point to H H O.	The xyz file has the following details about water molecule. 3, on the first line, is the number of atoms in the molecule. O H H are the symbols of the elements, oxygen and Hydrogen. They are positioned column-wise vertically.
Point to the numbers and xyz coordinates. Point to the values.	The numbers in rows are the xyz coordinates of the atoms, Oxygen, Hydrogen and Hydrogen. They are in Angstrom units. The values here are tab separated.
Point to the xyz coordinates of the molecule. Click on the X button to close	We got these xyz coordinates, after optimization of the molecule in Avogadro. Close the text document.
Cursor on Avogadro interface.	Back to the Avogadro interface. We will now generate an Orca input file.
On the Main menu bar Click on Extensions menu. Navigate to Orca From the Sub menu select Generate Orca Input option.	Click on the Extensions Menu and select Orca. From the Sub menu select Generate Orca Input option.
Point to the window. In the Comment field type Geometry Optimisation. Select Geometry Optimization in the Calculation drop down.	Orca Input Parameters window opens. In the comment field write Geometry Optimisation. In Calculation dropdown select Geometry Optimization.
In the Method drop down, Select RHF. Point to the option. Select def2-SVP from the Basis set drop down.	In the Method drop down Select RHF. RHF is the most conventional method for geometry optimization. Select the Basis set as def2-SVP.
Select Charge as 0 Multiplicity as 1	We will leave the Charge and Multiplicity values as default.
Point to the Multiplicity value 1 in the window..	Multiplicity of an energy level is defined as 2S+1. Here S is the total spin angular momentum. The Spin Angular momentum ( S ) is zero as there is no unpaired electron.
From the Format drop down select the format as Cartesian.	Select the format as Cartesian .
Highlight the input file in the Preview box. Click on the Generate button at the bottom of the window.	Now you can see the preview of the input file in the preview box. Click the Generate button at the bottom of the window.
Point to the Save Input Deck window. In the Name field filename water.inp appears	A Save Input Deck window opens. In the Name field the file name water.inp appears by default.
Select the water folder in the Home directory. Click on the Save button in the window.	Save the file in the water folder created in the Home directory. Click on Save button.
Click the Close button at the bottom right.	Click the Close button to close the Orca Input Parameters window.
Open the Home directory Open the water folder by double clicking on it.	Let us go back to the Home directory and open the water folder.
Point to the water.inp file in the folder. Right-click on the file to open it in gedit text editor.	It contains the wa ter.inp file. Let us open it using gedit text editor. This is the Orca input file . We have sucessfully generated the input file for Orca.
Only Narration	With this we come to the end of this tutorial. Let us summarize.
Slide Number 8 Summary	In this tutorial, we have, Created a 3D model of a molecule in Avogadro Optimized its geometry in Avogadro Measured the bond length and bond angle of the optimized molecule
Slide Number 9 Summary	Saved the structure in XYZ file format in a folder. Generated Orca input file for geometry optimization using Extensions menu.
Slide Number 10 Assignment	As an assignment, Practise drawing the structures of benzene and cyclohexane in Avogadro. Optimize the geometry of the molecules in Avogadro Save the structures in xyz file format. Generate Orca input files for geometry optimization of the molecules.
Slide Number 11 Spoken Tutorial Project	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide number 12 Spoken Tutorial workshop	The spoken tutorial project team conducts workshops and gives certificates. For more details, please write to us.
Slide number 13 Spoken Tutorial forum	Please post your timed queries in this forum.
Slide number 14 Acknowledgement	The Spoken Tutorial Project was established by the Ministry of Education Government of India.
Thank You	This tutorial is contributed by Rani Parvathy, Raj Singh and Madhuri Ganapathi from FOSSEE IIT Bombay. Thank you for joining.

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Madhurig, Snehalathak

Difference between revisions of "ORCA---Computational-Chemistry/C2/Creating-an-Input-File/English"

Revision as of 14:59, 29 September 2023

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