Avogadro/C4/File-Extensions/English - Revision history

Nancyvarkey at 09:03, 6 May 2016

2016-05-06T09:03:25Z

Show changes

Snehalathak at 10:44, 3 May 2016

2016-05-03T10:44:27Z

Snehalathak at 10:38, 3 May 2016

2016-05-03T10:38:11Z

Snehalathak: Created page with "{| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;b..."

2016-05-03T05:47:04Z

Created page with "{| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;b..."

New page

{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''File Extensions'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to,

* Prepare input files for '''computational '''<br/> '''chemistry''' programmes such as:<br/> '''GAMESS, Gaussian, MOPAC, NWChem''' <br/> etc.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * And view '''Molecular orbitals '''and''' calculated IR spectrum''' using output files generated from '''GAMESS''' and '''Gaussian''' software.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''

'''System Requirement'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I am using

'''Ubuntu Linux '''OS version. 14.04.

'''Avogadro v'''ersion 1.1.1.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''

'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with,

'''Avogadro''' interface.

If not, for relevant tutorials, please visit our website.

The example files required for this tutorial are provided as code files.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the slide.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Please download and save them in a folder on desktop.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open Avogadro window using dash home.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I have opened the '''Avogadro''' window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on build menu.

Scroll down to Insert then fragment.

Double click on aromatics folder and select '''benzene.cml''' file.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Load a benzene molecule from '''Build''' menu using '''Insert fragment''' library.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on auto-optimization tool.

In the auto-optimization settings,

change force-field to MMFF94.

Click on start.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Optimize the geometry using '''Auto-optimization tool''' from the tool bar.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the Extensions menu and scroll down.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the '''Extensions''' menu.

Using '''Avogadro''' we can prepare input files for popular quantum codes such as:

'''GAMESS'''

'''Gaussian'''

'''MOLPRO'''

'''MOPAC'''

'''Q-CHEM''' etc.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Gaussian.

Cursor on Gaussian input box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Gaussian''' option.

A graphical data input dialog box opens.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Gaussian input box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me demonstrate how to generate input file for '''Gaussian''' program.

We need to fill in the required features shown in the dialog box.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Gaussian input box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Avogadro''' by itself cannot calculate '''molecular orbitals.'''

So let us create an Input file to view the '''molecular orbitals''' of benzene molecule.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Gaussian input box.

Type the title as '''Benzene-MO'''.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In '''Gaussian''' input dialog box , type the title as '''Benzene hyphen MO'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Choose '''Frequencies''' from the '''Calculation''' drop-down.

Set 1 for the processors.

Theory as B3LYP.

Basis as 6-31G(d).

Charge zero.

Multiplicity 1.

Output as Standard.

Format as cartesian

Check the checkpoint check box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Choose '''Frequencies''' from the '''Calculation''' drop down.

'''Processors '''as '''1.'''

'''Theory '''as''' B3LYP.'''

'''6-31G(d) '''as''' Basis set.'''

'''Charge zero.'''

'''Multiplicity 1.'''

'''Output '''as '''Standard.'''

'''Format '''as '''cartesian'''

Check the''' checkpoint check box.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the text box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You can see the preview of the input file at the bottom of the dialog box.

It will be updated as you change the options.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Generate''' button.

A '''Save input Deck''' dialog box opens.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Generate''' button.

A '''Save input Deck''' dialog box opens.

The '''Gaussian input''' file generated will be saved with a '''dot com''' extension .

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type the file name as '''Benzene''', choose the location as '''Desktop'''.

Click on '''Save''' button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type the file name as '''Benzene.'''

Choose the location as '''Desktop'''.

Click on '''Save''' button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the file '''Benzene.com''' on the desktop.

Open '''Benzene.com. '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The file will be saved as '''Benzene.com''' on the desktop.

Open the file with '''gedit'''.

Now this file can be used as an input file for the '''Gaussian''' software programme.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''

'''Gaussian Software'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Gaussian''' software.

'''Gaussian''' is a computer programme for '''computational chemistry'''.

It is a commercial software developed and licensed by '''Gaussian Inc.'''

More information is available at the given link.

http://www.gaussian.com/

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on New from the tool bar.

Click on D'''raw''' '''tool'''.

In the draw settings select '''oxygen '''as element
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to '''Avogadro''' window.

Close the dialog box.

Now let us see how to prepare an input file for '''GAMESS''' programme.

Open a new window. Click on “'''New'''” from the '''Tools''' menu.

Build a water molecule using '''Draw tool'''.

Change the element to '''Oxygen'''.

Click on the panel.

Optimize the geometry using '''auto-optimization tool'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on extensions menu, select '''GAMESS''' Input generator from the submenu.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Extensions '''menu.

Select '''GAMESS, Input generator''' from the sub-menu.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''GAMESS-Input''' dialog box.

Cursor on tabs.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''GAMESS''' input dialog box opens.

There are two tabs '''Basic setup''' and '''Advanced setup'''.

As we did with the '''Gaussian '''input file, fill in the required information.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''Eqilibrium Geometry '''under''' Calculate.'''

'''RHF '''as '''With.'''

'''6-31G(d,p) '''as '''basis set.'''

'''In gas phase, singlet.'''

'''Charge''' as''' Neutral.'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Under Basic set up,

we will select '''Equilibrium Geometry '''under '''Calculate''' field.

'''RHF''', '''Restricted Hartee Fock''' method of '''approximation '''for the determination of '''wave function.'''

Since water is a small molecule, we will select '''6-31G(d,p)''' as basis set.

In''' gas''' phase, '''singlet''' , because all the electrons are paired.

Water is a neutral molecule, so''' charge''' will be '''neutral'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on''' advanced set up.'''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''advanced set up '''to add some more parameters to control the optimization.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on''' Basis.'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Basis '''if you want to change the set of functions.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Data.'''

Type the''' title '''as '''Benzene MO.'''

Type the''' Pointgroup '''as''' CnV.'''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Data.'''

Type the''' title''' as''' water-MO'''.

Change the '''Pointgroup''' to '''CnV'''.

'''Order of principal axis''' to '''2'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on''' Generate.'''

Cursor on the''' “Save input deck”.'''

Type the file name as''' water.'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For now we will keep the default parameters as such.

Click on '''Generate'''.

A '''Save input deck''' opens.

By default the file extension is '''dot''' '''inp'''.

Type the file name as '''water'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Choose the file location as '''Desktop'''.

'''Click on Save button.'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Choose the file location as '''Desktop'''.

Click on '''Save button.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Desktop.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The GAMESS input file is saved as '''Water.inp''' on the Desktop.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''

'''About GAMESS '''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''GAMESS'''
'''GAMESS''' stands for:
'''General Atomic and Molecular Electronic Structure System (GAMESS)''' It is a general '''ab initio quantum chemistry''' package.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''

'''About GAMESS '''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| It is available at no cost to both academic and industrial users.

Information about installation and download is given at the following link.

http://www.msg.ameslab.gov/gamess/download.html

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now we have generated input files for '''GAMESS''' and '''Gaussian''' programmes.

These input files are ready to be loaded into respective programmes.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''

'''Note for the viewers'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Viewers please note;

'''Gaussian''' is a commercial software.

Hence I will not be able to show the interface to load the input file.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''

'''Note for the viewers'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As mentioned earlier '''GAMESS''' is free software.

Those interested can download '''GAMESS''' software from the given link.

And Load the input file to generate the output file.

http://www.msg.ameslab.gov/gamess/download.htm

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have some '''Gaussian and GAMESS''' output files on the desktop.

I have provided these files as code files along with this tutorial.

Lets view these output files in '''avogadro'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Clck on open icon in the tool bar.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open a new Avogadro window.

Click on '''open''' icon in the tool bar.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Navigate to desktop files.

Select Benzene.log
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Navigate to the file location.

Select '''Benzene.log'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The file opens, we can see the structure of '''benzene''' on the panel.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Benzene.log''' was generated using '''Gaussian'''.

It contains information about '''molecular orbitals '''and '''C-C''' and '''C-H '''bond stretching.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Sometimes the log file may not show orbital information;

In such case open the '''.fchk '''file provided in the codefiles.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the orbital from the list.

Observe the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the '''orbitals,''' click on the orbital name from the list.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the '''spanner''' symbol next to surfaces option in the display types.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you want to change the display of '''orbitals'''.

Click on the '''spanner''' symbol next to surfaces option in the display types.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''Surface Setting''' dialog box.

Drag the '''slider''' to change the opacity.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the''' Surface Setting''' dialog box.

Drag the '''slider''' to change the opacity.

Observe the panel.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Render''' tab'''.'''

Click on''' lines'''.

Click on '''points option'''.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| There are three options in the '''Render''' drop-down, fill, lines and points.

By default the '''orbitals '''are rendered as '''fill'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the '''Color''' tabs next to '''positive''' and '''negative''' option.

A '''Select Color''' panel opens.

Click on '''OK''' button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| There is also an option to change the color of the lobes.

Click on the '''Color''' tabs next to '''positive''' and '''negative''' option.

A '''Select Color''' dialog box opens.

Click on any color to select.

Click on '''OK''' button.

Observe the panel, the colors of the orbitals are now changed.

Close the dialog box.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Uncheck the '''Surfaces''' option in the '''Display Types''' dialog box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To remove the orbitals from the structure;

Un-check the '''Surfaces''' option in the '''Display Types.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''vibrations''' tab.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Vibrations''' tab to view the '''vibrational frequencies. '''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on''' Vibration''' window.

Click on any frequency from the list.

Click on '''Start Animation''' button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the '''Vibration''' window, click on any frequency from the list.

Click on '''Start Animation''' button present at the bottom of the window.

Observe the panel.

The stretching of '''C-C''' and '''C-H''' bonds are animated.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Show Specta'''.

Cursor on '''Spectra Visualization''' window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also view the IR spectrum for the structure.

Click on '''Show Specta.'''

A '''Spectra Visualization''' window opens.

It shows the calculated''' IR spectrum''' of '''Benzene'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Navigate to the file on desktop using '''Open''' option in the tool bar.

Clik on '''H2O_6311+diff+DFTcorr.log''' file.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open a new window.

Open the '''log '''file created for water molecule using '''GAMESS''' programme.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The''' log '''file opens with a structure of water and Molecular orbital information.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the name of the '''orbital''' from the list.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the name of the '''orbital''' from the list.

The orbital is displayed on the panel.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 11'''

Summary
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let's summarize

In this tutorial we have learnt to,

Prepare the input files for '''computational chemistry''' programmes such as: '''GAMESS and Gaussian.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12'''

'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| View '''Molecular orbitals''' for '''benzene''' and '''water''' molecules.

View calculated '''IR spectrum''' for molecules using log files generated from '''Gaussian'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 13'''

Assignment
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For Assignment,

Open the log file for '''benzene''' molecule from the code files provided.

Display any '''Molecular Orbital''' from the list.

Change the display and color of the lobes.

Save the image in '''JPEG '''format.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 14'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * This video summarizes the Spoken Tutorial project
* If you do not have good bandwidth, you can download and watch it.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 15'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * We conduct workshops using Spoken Tutorials and give certificates.
* Please contact us.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 16'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 16'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from '''IIT Bombay''' signing off.

Thank you for joining.

|}

@@ Line 1: / Line 1: @@
+ {| style="border-spacing:0;"
 {| style="border-spacing:0;"
 ! <center>Visual Cue</center>
 ! <center>Narration</center>
@@ Line 657: / Line 656: @@
 Thank you for joining.
-|-
 |}

@@ Line 1: / Line 1: @@
 {| style="border-spacing:0;"
 ! <center>Visual Cue</center>
 ! <center>Narration</center>
 |-
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''
@@ Line 23: / Line 23: @@
 '''Learning Objectives'''
-| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * And view '''Molecular orbitals '''and''' calculated IR spectrum''' using output files generated from '''GAMESS''' and '''Gaussian''' software.
+| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * And view '''Molecular orbitals ''' and
 |-
@@ Line 236: / Line 240: @@
-Click on D'''raw''' '''tool'''.
+Click on '''Draw tool'''.
 In the draw settings select '''oxygen '''as element
@@ Line 261: / Line 265: @@
 Optimize the geometry using '''auto-optimization tool'''.
 |-
@@ Line 288: / Line 289: @@
-'''Eqilibrium Geometry '''under''' Calculate.'''
+'''Eqilibrium Geometry''' under '''Calculate'''.
@@ Line 358: / Line 359: @@
 A '''Save input deck''' opens.
-By default the file extension is '''dot''' '''inp'''.
+By default the file extension is '''dot inp'''.
@@ Line 378: / Line 379: @@
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''
-'''About GAMESS '''
+About '''GAMESS'''
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''GAMESS'''
 '''GAMESS''' stands for:
-'''General Atomic and Molecular Electronic Structure System (GAMESS)''' It is a general '''ab initio quantum chemistry''' package.
@@ Line 391: / Line 395: @@
 '''About GAMESS '''
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| It is available at no cost to both academic and industrial users.
@@ Line 480: / Line 481: @@
 Observe the panel.
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the '''orbitals,''' click on the orbital name from the list.
 |-
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the '''spanner''' symbol next to surfaces option in the display types.
@@ Line 515: / Line 512: @@
-By default the '''orbitals '''are rendered as '''fill'''.
+By default the '''orbitals ''' are rendered as '''fill'''.
 |-
@@ Line 567: / Line 564: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Show Specta'''.
+| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Show Spectra'''.
@@ Line 573: / Line 570: @@
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also view the IR spectrum for the structure.
-Click on '''Show Specta.'''
+Click on '''Show Spectra.'''
 A '''Spectra Visualization''' window opens.
@@ Line 583: / Line 580: @@
-Clik on '''H2O_6311+diff+DFTcorr.log''' file.
+Click on '''H2O_6311+diff+DFTcorr.log''' file.
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open a new window.
 Open the '''log '''file created for water molecule using '''GAMESS''' programme.
@@ Line 610: / Line 605: @@
 In this tutorial we have learnt to,
-Prepare the input files for '''computational chemistry''' programmes such as: '''GAMESS and Gaussian.'''
+Prepare the input files for '''computational chemistry''' programmes such as:
-−
-−
 |-
@@ Line 636: / Line 630: @@
 Save the image in '''JPEG '''format.
 |-
@@ Line 666: / Line 657: @@
 Thank you for joining.
+|-
 |}