Sandhya.np14 at 06:33, 24 July 2018

2018-07-24T06:33:27Z

Sandhya.np14 at 06:23, 6 June 2018

2018-06-06T06:23:25Z

Sandhya.np14 at 06:20, 6 June 2018

2018-06-06T06:20:16Z

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Jyotisolanki at 10:28, 8 December 2017

2017-12-08T10:28:36Z

PoojaMoolya: Created page with " {| border=1 | Time | Narration |- |00:01 | Welcome to this tutorial on '''File Extensions'''. |- |00:05 | In this tutorial, we will lear..."

2017-09-14T09:52:45Z

Created page with " {| border=1 | <center>Time</center> | <center>Narration</center> |- |00:01 | Welcome to this tutorial on '''File Extensions'''. |- |00:05 | In this tutorial, we will lear..."

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{| border=1
| <center>Time</center>
| <center>Narration</center>

|-
|00:01
| Welcome to this tutorial on '''File Extensions'''.

|-
|00:05
| In this tutorial, we will learn to, Prepare input files for '''computational ''' '''chemistry''' programmes such as:<br/> '''GAMESS, Gaussian, MOPAC, NWChem''' etc.

|-
|00:18
| And view '''Molecular orbitals ''' and '''calculated IR spectrum''' using output files generated from: '''GAMESS''' and '''Gaussian''' software.

|-
|00:28
| Here I am using '''Ubuntu Linux '''OS version. 14.04.

'''Avogadro''' version 1.1.1.

|-
|00:38
| To follow this tutorial you should be familiar with, '''Avogadro''' interface.

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|00:43
| If not, for relevant tutorials, please visit our website.

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|00:49
| The example files required for this tutorial are provided as code files.

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|00:55
| Please download and save them in a folder on desktop.

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|01:00
| Here I have opened the '''Avogadro''' window.

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|01:04
| Load a benzene molecule from '''Build''' menu using '''Insert fragment''' library.

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|01:12
| Optimize the geometry using '''Auto-optimization tool''' from the tool bar.

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|01:20
| Click on the '''Extensions''' menu.

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|01:23
|Using '''Avogadro''' we can prepare input files for popular quantum codes such as:

'''GAMESS'''

'''Gaussian'''

'''MOLPRO'''

'''MOPAC'''

'''Q-CHEM''' etc.

|-
| 01:36
| Click on '''Gaussian''' option.A graphical data input dialog box opens.

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|01:43
| Let me demonstrate how to generate input file for '''Gaussian''' program.

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|01:49
| We need to fill in the required features shown in the dialog box.

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| 01:55
| '''Avogadro''' by itself cannot calculate '''molecular orbitals.'''

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| 01:59
| So let us create an Input file to view the '''molecular orbitals''' of '''benzene''' molecule.

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|02:05
| In '''Gaussian''' input dialog box , type the title as '''Benzene hyphen MO'''.

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|02:11
| 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.'''

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|02:40
| You can see the preview of the input file at the bottom of the dialog box.

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|02:45
|It will be updated as you change the options.

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|02:49
| Click on '''Generate''' button.

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|02:52
|A '''Save input Deck''' dialog box opens.

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|02:56
|The '''Gaussian input''' file generated will be saved with a '''dot com''' extension .

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|03:02
| Type the file name as '''Benzene.''' Choose the location as '''Desktop'''. Click on '''Save''' button.

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|03:10
| The file will be saved as '''Benzene.com''' on the desktop. Open the file with '''gedit'''.

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|03:18
| Now this file can be used as an input file for the '''Gaussian''' software programme.

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|03: 24
| About '''Gaussian''' software.

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|03:28
|'''Gaussian''' is a computer programme for '''computational chemistry'''.

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|03:32
| It is a commercial software developed and licensed by '''Gaussian Inc.'''
More information is available at the given link. http://www.gaussian.com/

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|03:41
| Back to '''Avogadro''' window. Close the dialog box.

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|03:46
| Now let us see how to prepare an input file for '''GAMESS''' programme.

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|03:51
|Open a new window. Click on “'''New'''” from the '''Tools''' menu.

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|03:56
|Build a water molecule using '''Draw tool'''. Change the element to '''Oxygen'''.

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|04:01
|Click on the panel. Optimize the geometry using '''auto-optimization tool'''.

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|04:08
| Click on '''Extensions '''menu. Select '''GAMESS, Input generator''' from the sub-menu.

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|04:16
| A '''GAMESS''' input dialog box opens. There are two tabs '''Basic setup''' and '''Advanced setup'''.

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|04:24
|As we did with the '''Gaussian '''input file, fill in the required information.

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|04:29
| Under '''Basic Setup''', we will select '''Equilibrium Geometry '''under '''Calculate''' field.

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|04:36
|'''RHF''', '''Restricted Hartee Fock''' method of '''approximation '''for the determination of '''wave function.'''

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|04:44
|Since water is a small molecule, we will select '''6-31G(d,p)''' as '''Basis set.'''

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|04:52
|In''' gas''' phase, '''singlet''' , because all the electrons are paired.

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|04:58
|Water is a neutral molecule, so''' charge''' will be '''neutral'''.

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|05:02
| Click on '''Advanced Setup '''to add some more parameters to control the optimization.

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|05:08
| Click on '''Basis '''if you want to change the set of functions.

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|05:12
| Click on '''Data.'''

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|05:14
|Type the''' Title''' as''' water-MO'''.

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|05:18
|Change the '''Point Group''' to '''CnV'''.

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|05:21
|'''Order of Principal Axis''' to '''2'''.

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|05:24
| For now we will keep the default parameters as such.

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|05:29
|Click on '''Generate'''. A '''Save Input deck''' opens.

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|05:34
|By default, the file extension is '''dot inp'''.

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|05:38
|Type the file name as '''Water'''.

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|05:42
| Choose the file location as '''Desktop'''. Click on '''Save button.'''

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|05:48
| The '''GAMESS''' input file is saved as '''Water.inp''' on the '''Desktop'''.

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|05:55
| About '''GAMESS'''

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|05:57
| '''GAMESS''' stands for: '''General Atomic and Molecular Electronic Structure System'''.
(GAMESS)It is a general ab initio quantum chemistry package.

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|06:08
| It is available at no cost to both academic and industrial users.

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|06:14
| Information about installation and download is given at the following link. http://www.msg.ameslab.gov/gamess/download.html

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|06:20
| Now we have generated input files for '''GAMESS''' and '''Gaussian''' programmes.

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|06:26
|These input files are ready to be loaded into respective programmes.

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|06:31
| Viewers please note: '''Gaussian''' is a commercial software. Hence I will not be able to show the interface to load the input file.

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|06:41
| As mentioned earlier '''GAMESS''' is free software.

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|06:45
| 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

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|06:53
| I have some '''Gaussian and GAMESS''' output files on the desktop.

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|06:58
|I have provided these files as code files along with this tutorial.

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|07:03
|Lets view these output files in '''avogadro'''.

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|07:07
| Open a new Avogadro window.

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|07:10
| Click on '''open''' icon in the tool bar.

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|07:13
| Navigate to the file location. Select '''Benzene.log'''

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|07:18
| The file opens, we can see the structure of '''benzene''' on the panel.

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|07:24
| '''Benzene.log''' was generated using '''Gaussian'''.

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|07:28
|It contains information about '''molecular orbitals '''and '''C-C''' and '''C-H '''bond stretching.

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|07:36
| Sometimes the log file may not show orbital information.

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|07:40
|In such case open the '''.fchk '''file provided in the codefiles.

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|07:47
| To view the '''orbitals,''' click on the '''orbital''' name from the list.

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|07:54
| If you want to change the display of '''orbitals'''....

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

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|08:02
| In the''' Surface Setting''' dialog box.Drag the '''slider''' to change the opacity. Observe the panel.

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|08:10
| There are three options in the '''Render''' drop-down, fill, lines and points.

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|08:17
| By default the '''orbitals ''' are rendered as '''fill'''.

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|08:21
| There is also an option to change the color of the lobes.

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|08:25
| Click on the '''Color''' tabs next to '''positive''' and '''negative''' option.

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|08:30
| A '''Select Color''' dialog box opens.

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|08:33
| Click on any color to select. Click on '''OK''' button.

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|08:38
| Observe the panel, the colors of the orbitals are now changed. Close the dialog box.

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|08:45
| To remove the orbitals from the structure;Un-check the '''Surfaces''' option in the '''Display Types.'''

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|08:51
| Click on '''Vibrations''' tab to view the '''vibrational frequencies. '''

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|08:56
| In the '''Vibration''' window, click on any frequency from the list.

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|09:01
|Click on '''Start Animation''' button present at the bottom of the window.

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|09:06
|Observe the panel. The stretching of '''C-C''' and '''C-H''' bonds are animated.

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|09:13
| We can also view the IR spectrum for the structure.

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|09:17
| Click on '''Show Spectra.'''

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|09:20
| A '''Spectra Visualization''' window opens. It shows the calculated''' IR spectrum''' of '''Benzene'''.

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|09:27
| Open a new window. Open the '''log '''file created for water molecule using '''GAMESS''' programme.

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|09:35
| The''' log '''file opens with a structure of water and Molecular orbital information.

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|09:41
| Click on the name of the '''orbital''' from the list. The orbital is displayed on the panel.

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|09:47
| Let's summarize

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|09:49
| In this tutorial we have learnt to, Prepare the input files for '''computational chemistry''' programmes such as: '''GAMESS and Gaussian.'''

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|09:58
| View '''Molecular orbitals''' for '''benzene''' and '''water''' molecules.

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|10:04
| View calculated '''IR spectrum''' for molecules using log files generated from '''Gaussian'''.

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|10:11
| For Assignment, Open the log file for '''benzene''' molecule from the code files provided.

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|10:18
| Display any '''Molecular Orbital''' from the list.

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|10:22
| Change the display and color of the lobes. Save the image in '''JPEG '''format.

|-
|10:29
| This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.

|-
|10:35
| We conduct workshops using Spoken Tutorials and give certificates. Please contact us.

|-
|10:42
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.

|-
|10:48
| This is Snehalatha from '''IIT Bombay''' signing off.

Thank you for joining.

|}

@@ Line 89: / Line 89: @@
 |-
 |02:05
-|  In '''Gaussian''' input dialog box , type the title as '''Benzene hyphen MO'''.
+|  In '''Gaussian''' input dialog box , type the '''Title''' as '''Benzene hyphen MO'''.
 |-

@@ Line 144: / Line 144: @@
 |-
-|03: 24
+|03:24
 |  About '''Gaussian''' software.
@@ Line 153: / Line 153: @@
 |-
 |03:32
-| It is a commercial software developed and licensed by '''Gaussian Inc.'''
+| It is a commercial software developed and licensed by '''Gaussian Inc.''' More information is available at the given link. http://www.gaussian.com/
 More information is available at the given link. http://www.gaussian.com/
 |-
@@ Line 292: / Line 291: @@
 |-
 |06:45
-| Those interested can download '''GAMESS''' software from the given link.
+| Those interested can download '''GAMESS''' software from the given link. And, load the input file to generate the output file.
 And load the input file to generate the output file.
 http://www.msg.ameslab.gov/gamess/download.htm
@@ Line 347: / Line 345: @@
 |07:54
 |  If you want to change the display of '''orbitals''',
 click on the '''spanner''' symbol next to surfaces option in the display types.

@@ Line 354: / Line 354: @@
 |-
 |08:10
-|  There are three options in the '''Render''' drop-down, fill, lines and points.
+|  There are three options in the '''Render''' drop-down, '''fill''', '''lines''' and '''points'''.
 |-

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

Sandhya.np14 at 06:33, 24 July 2018

Sandhya.np14 at 06:23, 6 June 2018

Sandhya.np14 at 06:20, 6 June 2018

Jyotisolanki at 10:28, 8 December 2017

PoojaMoolya: Created page with " {| border=1 | Time | Narration |- |00:01 | Welcome to this tutorial on '''File Extensions'''. |- |00:05 | In this tutorial, we will lear..."