ORCA---Computational-Chemistry/C2/Creating-an-Input-File/English
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,
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Slide Number 3
Learning Objectives |
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Slide Number 4
System Requirements |
To record this tutorial, I am using;
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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.
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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.
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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.
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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.
Select Avogadro from the shown list. |
Click the displayed Avogadro icon to open the application.
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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.
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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.
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From the Force Field drop-down select the MMFF94 option.
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Point to the molecule in the panel.
In the panel, we see dE =0.
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.
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Cursor on water molecule.
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.
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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)
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Click on the second hydrogen atom
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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.
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Click the File menu and select Save As option.
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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.
Double-click the folder to open it. |
A new folder appears in the dialog box.
Then double-click the water folder to open it.
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In the File name field, type filename as water.xyz
In the Files of type, drop-down select XYZ file format.
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In the Filename field type the filename as water.xyz.
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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.
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Point to 3.
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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.
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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.
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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.
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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.
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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.
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Now you can see the preview of the input file in the preview box.
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Point to the Save Input Deck window.
In the Name field filename water.inp appears |
A Save Input Deck window opens.
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Select the water folder in the Home directory.
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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 water.inp file.
Let us open it using gedit text editor.
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
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In this tutorial, we have,
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Slide Number 9
Summary |
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Slide Number 10
Assignment |
As an assignment,
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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.
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