Snehalathak at 03:32, 10 October 2023

2023-10-10T03:32:51Z

Madhurig: Created page with "'''Title of the script''': Creating an Input File '''Author''': Madhuri Ganapathi, Rani Parvathy, Raj Singh, Arup Sarkar. '''Keywords''': Avogadro, gedit text editor, auto..."

2023-09-29T09:29:13Z

Created page with "'''Title of the script''': Creating an Input File '''Author''': Madhuri Ganapathi, Rani Parvathy, Raj Singh, Arup Sarkar. '''Keywords''': Avogadro, gedit text editor, auto..."

New page

'''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.

{| border=1

||'''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 Edito'''r 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 104.0<sup>0</sup> 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.
|-
|}

@@ Line 454: / Line 454: @@
 Right-click on the file to open it in '''gedit '''text editor.
-||It contains the '''wa ter.inp''' file.
+||It contains the '''water.inp''' file.
 Let us open it using '''gedit''' text editor.

ORCA---Computational-Chemistry/C2/Creating-an-Input-File/English - Revision history

Snehalathak at 03:32, 10 October 2023

Madhurig: Created page with "'''Title of the script''': Creating an Input File '''Author''': Madhuri Ganapathi, Rani Parvathy, Raj Singh, Arup Sarkar. '''Keywords''': Avogadro, gedit text editor, auto..."