Difference between revisions of "Avogadro/C4/File-Extensions/English"

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{| style="border-spacing:0;"
 
{| style="border-spacing:0;"
 
! <center>Visual Cue</center>
 
! <center>Visual Cue</center>
 
! <center>Narration</center>
 
! <center>Narration</center>
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| 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'''
 
| 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'''
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'''Learning Objectives'''
 
'''Learning Objectives'''
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| 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.
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| 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  
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'''calculated IR spectrum''' using output files generated from:
  
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* '''GAMESS''' and
  
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* '''Gaussian''' software.
  
 
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Click on D'''raw''' '''tool'''.  
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Click on '''Draw tool'''.  
  
 
In the draw settings select '''oxygen '''as element
 
In the draw settings select '''oxygen '''as element
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Optimize the geometry using '''auto-optimization tool'''.
 
Optimize the geometry using '''auto-optimization tool'''.
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−
 
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'''Eqilibrium Geometry '''under''' Calculate.'''
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'''Eqilibrium Geometry''' under '''Calculate'''.
  
  
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A '''Save input deck''' opens.
 
A '''Save input deck''' opens.
  
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By default the file extension is '''dot''' '''inp'''.
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By default the file extension is '''dot inp'''.
  
  
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| 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'''
 
| 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'''
  
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'''About GAMESS '''
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About '''GAMESS'''
  
  
  
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| 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'''  
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| 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:  
 
'''GAMESS''' stands for:  
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'''General Atomic and Molecular Electronic Structure System (GAMESS)''' It is a general '''ab initio quantum chemistry''' package.  
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'''General Atomic and Molecular Electronic Structure System'''.
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(GAMESS)It is a general ab initio quantum chemistry package.
  
  
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'''About GAMESS '''
 
'''About GAMESS '''
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−
 
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| 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.
 
| 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.
  
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Observe the panel.
 
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:1pt solid #000000;padding:0.097cm;"| To view the '''orbitals,''' click on the orbital name from the list.
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| 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:none;padding:0.097cm;"| Click on the '''spanner''' symbol next to surfaces option in the display types.
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By default the '''orbitals '''are rendered as '''fill'''.
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By default the '''orbitals ''' are rendered as '''fill'''.
  
 
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|-
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| 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'''.
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| 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'''.
  
  
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| 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.
 
| 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.
  
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Click on '''Show Specta.'''
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Click on '''Show Spectra.'''
  
 
A '''Spectra Visualization''' window opens.
 
A '''Spectra Visualization''' window opens.
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Clik on '''H2O_6311+diff+DFTcorr.log''' file.
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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.
 
| 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.
 
Open the '''log '''file created for water molecule using '''GAMESS''' programme.
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In this tutorial we have learnt to,
 
In this tutorial we have learnt to,
  
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Prepare the input files for '''computational chemistry''' programmes such as: '''GAMESS and Gaussian.'''
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Prepare the input files for '''computational chemistry''' programmes such as:
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+
−
 
+
  
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* '''GAMESS and Gaussian.'''
  
 
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Save the image in '''JPEG '''format.
 
Save the image in '''JPEG '''format.
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Thank you for joining.  
 
Thank you for joining.  
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Revision as of 16:08, 3 May 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on File Extensions.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Prepare input files for computational
    chemistry programmes such as:
    GAMESS, Gaussian, MOPAC, NWChem
    etc.


Slide Number 3

Learning Objectives

* And view Molecular orbitals and

calculated IR spectrum using output files generated from:

  • GAMESS and
  • Gaussian software.
Slide Number 4

System Requirement

Here I am using

Ubuntu Linux OS version. 14.04.

Avogadro version 1.1.1.

Slide Number 5

Pre-requisites

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.

Cursor on the slide. Please download and save them in a folder on desktop.
Open Avogadro window using dash home. Here I have opened the Avogadro window.
Click on build menu.

Scroll down to Insert then fragment.

Double click on aromatics folder and select benzene.cml file.

Load a benzene molecule from Build menu using Insert fragment library.



Click on auto-optimization tool.

In the auto-optimization settings,

change force-field to MMFF94.

Click on start.

Optimize the geometry using Auto-optimization tool from the tool bar.
Click on the Extensions menu and scroll down. 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.

Click on Gaussian.


Cursor on Gaussian input box.

Click on Gaussian option.


A graphical data input dialog box opens.



Cursor on Gaussian input box. Let me demonstrate how to generate input file for Gaussian program.


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

Cursor on Gaussian input box. Avogadro by itself cannot calculate molecular orbitals.


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

Cursor on Gaussian input box.

Type the title as Benzene-MO.

In Gaussian input dialog box , type the title as Benzene hyphen MO.



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.

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.

Cursor on the text box. 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.

Click on Generate button.

A Save input Deck dialog box opens.

Click on Generate button.

A Save input Deck dialog box opens.


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

Type the file name as Benzene, choose the location as Desktop.


Click on Save button.

Type the file name as Benzene.

Choose the location as Desktop.


Click on Save button.

Cursor on the file Benzene.com on the desktop.

Open Benzene.com.

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.



Slide Number 6

Gaussian Software

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/

Click on New from the tool bar.


Click on Draw tool.

In the draw settings select oxygen as element

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.

Click on extensions menu, select GAMESS Input generator from the submenu. Click on Extensions menu.

Select GAMESS, Input generator from the sub-menu.

Cursor on the GAMESS-Input dialog box.


Cursor on tabs.

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.

Type,


Eqilibrium Geometry under Calculate.


RHF as With.


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

In gas phase, singlet.

Charge as Neutral.

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.

Click on advanced set up.


Click on advanced set up to add some more parameters to control the optimization.
Click on Basis. Click on Basis if you want to change the set of functions.
Click on Data.

Type the title as Benzene MO.

Type the Pointgroup as CnV.


Click on Data.

Type the title as water-MO.

Change the Pointgroup to CnV.

Order of principal axis to 2.

Click on Generate.


Cursor on the “Save input deck”.


Type the file name as water.

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.

Choose the file location as Desktop.

Click on Save button.

Choose the file location as Desktop.

Click on Save button.

Cursor on Desktop. The GAMESS input file is saved as Water.inp on the Desktop.
Slide Number 7

About GAMESS


About GAMESS

GAMESS stands for:

General Atomic and Molecular Electronic Structure System.

(GAMESS)It is a general ab initio quantum chemistry package.


Slide Number 8

About GAMESS

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

Cursor on the panel. Now we have generated input files for GAMESS and Gaussian programmes.


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

Slide Number 9

Note for the viewers

Viewers please note;

Gaussian is a commercial software.

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

Slide Number 10

Note for the viewers

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

Cursor on the panel. 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.

Clck on open icon in the tool bar. Open a new Avogadro window.


Click on open icon in the tool bar.

Navigate to desktop files.

Select Benzene.log

Navigate to the file location.

Select Benzene.log

Cursor on the panel. The file opens, we can see the structure of benzene on the panel.



Benzene.log was generated using Gaussian.


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

Cursor on the panel. Sometimes the log file may not show orbital information;

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

Click on the orbital from the list.

Observe the panel.

To view the orbitals, click on the orbital name from the list.
Click on the spanner symbol next to surfaces option in the display types. If you want to change the display of orbitals.


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

Cursor on the Surface Setting dialog box.


Drag the slider to change the opacity.

In the Surface Setting dialog box.


Drag the slider to change the opacity.


Observe the panel.

Click on Render tab.


Click on lines.


Click on points option.

There are three options in the Render drop-down, fill, lines and points.


By default the orbitals are rendered as fill.

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


A Select Color panel opens.


Click on OK button.

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.

Uncheck the Surfaces option in the Display Types dialog box. To remove the orbitals from the structure;


Un-check the Surfaces option in the Display Types.

Click on vibrations tab. Click on Vibrations tab to view the vibrational frequencies.
Cursor on Vibration window.


Click on any frequency from the list.


Click on Start Animation button.

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.

Click on Show Spectra.


Cursor on Spectra Visualization window.

We can also view the IR spectrum for the structure.

Click on Show Spectra.

A Spectra Visualization window opens.

It shows the calculated IR spectrum of Benzene.

Navigate to the file on desktop using Open option in the tool bar.


Click on H2O_6311+diff+DFTcorr.log file.

Open a new window.

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


Cursor on the panel. The log file opens with a structure of water and Molecular orbital information.
Click on the name of the orbital from the list. Click on the name of the orbital from the list.


The orbital is displayed on the panel.

Slide Number 11

Summary

Let's summarize

In this tutorial we have learnt to,

Prepare the input files for computational chemistry programmes such as:

  • GAMESS and Gaussian.
Slide Number 12

Summary

View Molecular orbitals for benzene and water molecules.

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

Slide Number 13

Assignment

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.

Slide Number 14

Acknowledgement

* This video summarizes the Spoken Tutorial project
  • If you do not have good bandwidth, you can download and watch it.


Slide Number 15 * We conduct workshops using Spoken Tutorials and give certificates.
  • Please contact us.


Slide number 16 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
Slide number 16 This is Snehalatha from IIT Bombay signing off.


Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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